The Menus:

File: You can only open a file of three specific formats. You can Open
  Locomotive and Save Selected Locomotive data that you changed in
  the locomotive setup dialog and programming dialog. It will only
  save the one "selected" locomotive indicated on the DCC window. You
  can save an individual loco so you can have more locomotives
  defined than you would use during a particular operating session.
  New locos are added to the first window with an empty space. *Note
  that if there are already the maximum number of locomotives
  displayed, the new loco will delete the last defined locomotive.
  See the Loco menu for the order of creation.
  Accessories are handled the same as locomotives with the Open
  Accessory and Save Selected Accessory menu items.
  An entire roster of several locos and accessories can be opened and
  saved as well with the Open Setup... and Save Setup... commands.
  The window locations are restored, but the clock data is not (yet).
  The program forces you to save the name of the setup file each time
  so that you can have multiple operating sessions with different
  rosters of locomotives. Some might call this a bug, but I think of
  it as a feature.
  Note: The locomotive programming information is saved with either
  the individual loco or the setup, but if you open a setup after
  making changes to an individual loco file, the changes will NOT be
  loaded. You will want to delete the setup file's loco and then open
  the individual loco file. If you make changes to a loco while an
  entire setup is open you should save the individual loco data as
  well as the setup.
  You can also Quit the program. Always useful if you want to do
  something else.

Edit: There isn't anything to edit yet, so it is disabled except for
  textedit boxes that the system handles on its own.

Clock: There are 6 sub-menus here.
  Clock Style lets you display seconds, no seconds, 12 hour AM/PM
  mode or 24 Hour mode. The window will be resized automatically if
  you change the clock style. This lets you have a nearly full screen
  display if you use 24 Hour mode without seconds. So far you only
  have a digital display. I may add an analog display option later,
  again you need to let me know you want it or it may not happen.
  
  Start Time lets you specify the time to be displayed. The default
  time is local time, set via the General control panel or other time
  keeping program. If you have the Map control panel, you can specify
  where you are on the globe, so that Greenwich Mean Time will be
  correct. If you choose this option and the time stays the same, you
  don't have the Map control panel or you live in the GMT time zone.
  You can also set the start time to be any whole hour between
  Midnight and Eleven PM. This menu changes to reflect whether you
  have time displayed as AM/PM or as 24 hour mode.
  
  Clock Speed: To change the clock speed you must have specified the
  start time to be between Midnight and 11:00 PM. If you display
  Local time or GMT, you are stuck with real-time just like the rest
  of us. You can get up to 20:1 performance if you choose a start
  time. Command key equivalents have been set up for the first ten
  speeds (cmd-1 thru cmd-0). You can also pause the time (cmd-P)
  (again not Local or GMT) if you need to go answer the phone or
  answer the call of nature in the middle of an operating session.
  
  Text menus: You will find that you can change the font, size and
  style of the numbers displayed. The program will automatically
  resize the window for you centered about the present location of
  the window. If you move the window via the drag bar, then the
  window will stay there and any more changes requiring a new window
  size will be centered about the new location. The program will
  think awhile about what size fonts it can handle on the screen and
  will make the size menu change to indicate the largest size that
  will fit on the main screen.
  
Acc's menu:
  When you select the accessory you want to modify, a dialog box will
  come up with various items to change for that accessory. See the
  Setup menu description below for details. Double clicking on a non-
  control area of an accessory will also open this dialog window.
  
Loco menu:
  When you select the locomotive you want to modify, a dialog box
  will come up with various items to change for that locomotive. See
  the Setup menu description below for details. Double clicking on a
  non-control area of a locomotive will also open this dialog window.
  
Setup menu:
  Add Locomotive...: Lets you add another locomotive to the roster.
  You can add locos, and delete them. You are limited to 40 at a time
  if you have a 16" monitor, 30 at a time with a 13" monitor, and 25
  at a time with a 9" monitor. The dialog box lets you change the
  road name and number of the loco and the type of decoder installed.
  The road name and number is displayed on the Loco window so you can
  easily see what loco you are controlling instead of converting a
  channel number in your head. You should limit the number of
  characters to 9 on each line or they will be cut off. Use Shift-
  Return to add a new line in the textedit box rather than leaving
  the dialog. The channel number can be changed if it was
  reprogrammed elsewhere, and it will change if you program a new
  channel number using the programming dialog.
  There are 5 speed options for your decoders. Basic 14 speeds,
  Extended 28 speeds, Advanced 128 speeds and two special 28 speed
  and 56 speed modes. The special interpolated speeds are done by
  sending either the 14 speed or 28 speed packets about 25 times each
  second, but bouncing between two different speeds so that the
  decoder ends up averaging the two speeds. Program in some momentum
  to the decoder to make it smoother. Beware that too much momentum
  makes the trains start and stop slowly just like the real thing.
  Emergency Stop is the Space Bar!
  You can specify which window and where on the window the new
  locomotive will go. This comes in handy if you have a set of locomotives you
  want to set up to run together.

  The MU Setup... button is for running multiple locomotives with one
  slider bar control. Say you want to put a loco in the lead that has
  channel 45, then when you can add other locos with different
  channel numbers, set their MU channel to 45, and they will be
  slaved to the lead locomotive. You need to specify which direction
  the loco is facing. This direction is dependent on the lead loco,
  so pay attention to which direction the lead is set to before
  setting this. Once a loco is slaved, you can only control the
  consist speed and direction from the lead loco. If you want to
  match speeds with different locos, then time your locos at 14 speed
  steps by setting up a loop of track to run around on. Press each
  Test button in turn to time the loco. Press Stop when the loco
  reaches the same spot. The program will convert the time it takes
  to complete the loop into scale miles per hour for each speed step.
  The lead loco will search for slaves and find the closest speed
  step to match. Since a 28 speed decoder has finer control, it is
  recommended that you use a 14 speed loco in the lead so the slaves
  can better match the lead loco. But... If one loco has a much
  faster top speed consider putting the 28 speed decoder in it, so
  the finer control can be used at the low speed settings where it is
  useful.  The best solution is to use decoders with the 28 speed
  table implemented in the configuration variables. This allows you
  to set the loco speeds in the decoders and run your loco on other
  layouts without tying you to this program.  You can also MU two
  locos by draging the slave onto the lead on the loco windows. To un-
  MU a locomotive, drag the slave's box up to where a normal loco
  would be drawn.
  The Functions... button allows special effects for each of the
  functions which may not yet be implemented on the decoder. A
  flashing function is set by setting the check box to enable the
  control and the check box to enable flashing. Set the time on and
  off in integer units of 1/60 of a second. Default is no flashing
  and 30/60th (1/2 second). There are two sets of on and off times,
  to give you something like a Mars light effect. Try 20, 20, 20, 40.
  You can set the name of the function for display on the Loco
  window. Use Shift-Return to add a second line of text to that
  function.
  Note that the directional light uses function 5 of group 1 while in
  extended 28 speed, and basic 14 speed packets use function 0 for
  directional lights. Both of these are mapped to function 0 (or FL)
  in this program. If you use 14 speed mode or 28 speed mode, the
  program will use the appropriate function packet. If your head
  light turns on and off when increasing speed, then your loco thinks
  you are sending basic 14 speed packets when the program is sending
  extended 28 speed packets. The bit that turns on the head lights in
  14 speed mode is also used to give you the extra speeds in 28 speed
  mode. If you are not getting the fine speed control you think you
  should and the head light does not come on, then the program may be
  sending 14 speed packets instead of 28.  Newer decoders that adhere
  better to the standard and RP's will use function 5 for 14 speeds
  as well as 28 speeds, but the program will not turn on the function
  5 bit. Just use 28 speed, it works.
  The first five functions are latched, so that each time a loco
  packet is refreshed (by changing speed or every 1/2 second or so
  with no activity) the function value is sent again.  The final four
  functions are momentary (hence the button instead of a check box)
  Only one packet to that function is sent when the button is
  pressed. These are designed as triggers for sound effects more than
  as lights which would be constantly on.  I don't have a decoder to
  test this, so if you do, let me know if it works or not.
  
  Add Accessory... works very similar to the locomotive dialog,
  except you only have functions to modify.  I have implemented 6 bit
  addressing to stay consistent with the decoders available now.
  Lenz T001-, T001+ and Digitrax 1-t, 1-c are the same functions. If
  you set the dialog box up to have any address between 1 and 4, it
  will be displayed as Addr: 1-4 on the accessory control window.
  There are 8 functions per set, but they are in pairs, such that
  enabling one function of the pair disables the other. It should be
  obvious when you play with the radio buttons.  The RP's leave open
  the possibility of having 8 independant functions whenever someone
  produces a decoder that behaves that way. I have provided basic
  support for this by allowing you to turn off the paired action.
  Note that there will be no packet sent to turn off the individual
  functions. The decoder will have to do that for now. You can make
  the functions flash on and off (or switch a turnout back an forth
  if you have some bizarre need) by setting the on off text boxes to
  integer values as with the loco functions.
  
  Transmit Data turns on packets to the serial port. The first time
  the program attempts to send data, the port setup dialog will come
  up (see below). If there are no locomotives nor accessories
  defined, then idle packets will be sent.
  
  The Port Setup... dialog lets you toggle between the modem port and
  the printer port. The other buttons let you set the baud rate. 52
  microseconds is the default and seems to work well.
  
  Program Register... is used to change the decoders' default settings. 
  
Remember to isolate all other locos and accessory decoders from the programming track or you will program them too.
                                   
  Set the value you want in the text edit box and press the Write
  button next to the item to change. The program will remember the
  full page range of 128 values. (Remember to "save" your loco setup
  to retain these new values.) When you press the program button, the
  computer will send reset packets, then programming packets, then
  turn off packet transmission to the loco(s) on the track. You may
  hear the loco make a chirping sound if it was successful. The
  choices for the different decoders allows you to see what
  configuration variables are mapped to which address. Paging is
  supported for the Digitrax decoder type. If you don't program the
  page value before programming what is displayed in the first 4
  registers, the new page will be done first automatically.
  The Read buttons do not work yet as I have not added decoder
  feedback.
  Each bit can be set for a configuration variable by pressing the
  Set Bits... button next to each variable. This allows you to see
  what each bit does and makes it more convienient than having to
  manually add up 1+8+32+128 to set those 4 bits.  No description
  means there is no meaning for individual bits for that
  configuration variable.
  Write All and Read All also are not implemented, but when they are,
  they will only read and write the eight data displayed.
  
  Background Friendly gives background tasks the recommended amount
  of time to continue running, but if you have a slow Macintosh, or
  are only running in Finder and not MultiFinder, then you will get
  better flash rate performance with Background Unfriendly or
  Background Hostile, which gives little time to background tasks.
  
  To further speed things up, the last item allows you to turn off the
  refresh of the status window with information about packets being sent.
  
Windows menu
  This allows you to bring to front each window, or unhide a window
  that was closed. Remember that if there is no locomotive or
  accessory defined, then these windows will not appear.  I should
  make the windows dynamic, so that memory is not used on a window
  definition if there are no locos or accessories for that window,
  but that will have to wait until the next version. Can you say
  'Hobby pursuits come in last in the priority list'?