When you run a fresh, new copy of Pearl, it detects this an gives you the option to be guided through a new-user set-up (which is probably how you got to be reading this text).  The description below assumes that you have gone through that set up and have at least one archive already created automatically by Pearl.

Once you've gone through the new user set up, the next thing to do is set the preferences.  It's important to realize that each copy of Pearl contains it's own internal preferences, there is not a general preferences file in the Preferences folder of the System folder.  This lets you keep more than one copy of Pearl around, each configured a particular way for a particular job (or you can just have one, if that's the way you want to work).  To set Pearl's preferences, choose Preferences... from the Edit menu.

You'll see a variety of preferences to set, which the new-user set-up has set to defaults.  The first two are sliders that vary between "Never" and "Always".  The first slider is labled "Prompt for description".  By adjusting it between the extremes, you tell Pearl how much you trust it to deduce the description of a given piece of text.  If you set the slider to "Always", Pearl will always present new text to you in a New Item window and allow you to edit it and it's description before the text is archived (unless you use the Paste to Archive item in the Edit menu, that always does just what it says).  This can interrupt the flow of your work, but it's a good setting for those who want to be distincly aware of everything they archive Pearl.  Setting this slider to "Never" will put Pearl in automatic mode, never interrupting you.  In between, Pearl will prompt you or not, depending on it's confidence in the description it has deduced.

Second, there is a slider labeled "Normalize Text".  This slider tells Pearl how agressive it should be in removing junk from text it archives.  If you set it to "Never", text will be archived unchanged.  If you set it to "Always", text will be stripped of anything the least bit unusual or un-Mac-like and lines of text will be flowed into paragraphs that might not be what was intended.  Most people will do best by leaving this slider around the middle.

The sound settings are self-explainatory.  Pearl's sounds are the most useful if it is to be run in automatic mode, when the sounds can tell you what's going on without stopping to show you anything or require you click an OK button.  The sounds are much faster than the voice messages, but they're more cryptic and contain less information.  The voice messages are experimental, really.  Future versions of Pearl will be better about voice messages (and sound in general), but, for now, they're pretty annoying.

The Quick Menu items are a bit tricky.  They let you really speed up the way you use Pearl day-to-day, but you pay for this by having to read this paragraph.  The Quick Menu items are archives that this particular copy of Pearl is going to work most closely with. If you press the Edit Items button, you'll get another dialog that will let you add up to eight archives to a list, by picking them from a Standard File dialog (of course, if you only have one archive at this point, there's not much to do).  Each time you click the Add button, a Standard File dialog will come up and let you pick another archive from the file system.  Clicking in the "Default" column will put a checkmark next to the archive you want to be the default when Pearl is run in automatic mode.  If you don't specify a default, Pearl won't run in automatic mode.  Once you have set up the Quick menu items, you'll notice that the Quick Open and Quick Save items in the File menu have sub-menus with your archives listed.  This avoids going through a standard file dialog to open and archive or save a new item to an archive and saves a lot of time.  The default item will have it's own command key in the Quick Save dialog, making it a single command-key to save a new item to the default archive.  Since many people will have fewer than eight archives total, you may never have to use Standard File within Pearl again!  The new-user set-up will have placed your first archive in the Quick Menu list and made it the default.  If you don't want to use the Quick Items, you don't have to.  New Items can be saved to an archive by picking Save... from the Edit menu.  This will give you a Standard File dialog and allow you to select an archive (but it's a lot slower than just picking the item from the Quick Menu).  If you're confused at this point, just don't change anything, the new-user set-up has it all fixed for you.

The "Default text style" settings tell Pearl what style you wish to see text displayed in that has no style of it's own.  Most commumnications programs, for example, only put text information on the clipboard, with no style information.  Pearl examines each chunk of text it is archiving.  If the chunk has no style information at all, or if the entire chunk is in one style, Pearl converts it to the default you specify in the preferences.  If the text has styles, Pearl keeps them just the way they are.

Later on you can make more copies of Pearl, each with it's own settings, that point to whichever archives you like.  If you want to keep it simple to start, create one copy of Pearl and use the archive created in the new-user set-up.  You can always go crazy later on.

This flexibility is one of Pearl's design goals.  You can, for example, put aliases to two copies of Pearl in your Apple Menu Items folder.  One can be set for interactive operation, where you always get to edit the item before it's archived, the other can be set to automatically archive as fast as possible.  Then you can pick the one that suits your needs of the moment.