MacMod Pro's preferences are divided into six groups:  General, Editor, Playing,  Staff, Keyboard, and Other.

Folders:
This is where you can select default folders for opening and saving songs (MODs), instruments, patterns, music lists, and plug-ins.

Editor:
Here you choose what want MacMod Pro does at startup.  If you run MacMod Pro by openning a song, it will do nothing but open that song upon startup.  The default pasting volume is the volume that will be set when you paste an instrument from a clipboard.  The default number of voices is the number that will be displayed in the ‘New Mod’ dialog.  You can also choose whether you want the popup menu for selecting instruments in the standard editor to use a smaller font (geneva size 10) than the normal menu font.

Playing:
Here you can choose to repeat a song after playing it or go on to play the next song in the Music Dektop's list.  You can also specify if you want to use stereo and surround sound.  If you computer does not support stereo, these two items will be dimmed.  There are controls to allow you to fade out the music when a song stops playing and to end infinite playing loops.

Staff:
There are controls for setting the default key signature displayed in the staff editor and for setting the default base octave.  This control determines the octave range displayed in the staff editor.

Keyboard:
This section contains controls for setting keyboard equivalents to keys in the Keyboard window.

Other:
This is where you can choose what you want MacMod Pro to do when you remove an unsaved song from the Music Desktop's list.  You can also specify whether you want MacMod Pro to alert you when deleting instruments or clearing sequence slots.  There is also a new feature called ‘Auto Save’ which allows you to save the current song at regular time intervals.