Preferences objects are created by default when you start a new GBS. Preferences files are reparsed every time you call "Start GBS", so if the program doesn't seem to be recognizing your Preferences changes, restart the GBS.
In the GBS, resource files are kept open as little as possible. If they get stuck open (i.e. ResEdit claims the file is currently in use), go to the Messages window and type (close-rsrc-file) and press return. If you see a t, that means you just closed the resource file and you're all set.
Resource files need to have either no extension or the extension ".rsrc" (lower case).
To edit your gbs-preferences, go to the "Objects" menu, and choose "GBS Preferences", then double click on the preferences object in the window that appears.
This order is accessed by the Go To Next Scenario model action.
If you call "go to next scenario" and you've run out of scenarios, you'll get a dialog telling you as such. If you'd like to have some sort of wrap-up, make a wrap-up-scenario upon whose choosing you start the wrap-up phase.