Scott-
I assign different functions to the pedals for each song! For some songs, I use the fill-ins a lot; others require a fade-out ending; others require incremental movements in the panel memory! So, I set up the entire keyboard and then save those settings to a song-particular file on disk. Then, I mark up my sheet music with colored squares to indicate which pedal to hit when. (I used the colored stickers that came with the pedals - blue is 1, yellow is 2, green is 3 and red is 4.) This only works, of course, if you are playing from sheet music. Memorizing this all would be next-to-impossible!
I don't have a hard disk (yet!), so I save my song settings in one of 4 categories, each of which has 20 diskettes; for instance, "All of Me" would be on disk Jazz-A, while "Billie Jean would be on "Rock-B" and "Getting to Know You" is on "Broadway&TV-G" - it makes for QUITE a collections of "floppies"! Then, once I have put a show together, I create a disk just for that show, in sequence, with a matching binder of sheet music with clear "disk instructions" on top. It cuts down on spontaneity and the ability to take requests, that's for sure! However, I discovered that almost all my "embarassing moments while performing" were caused not by hitting the wrong keys, but by hitting the wrong BUTTONS! My system has cut down on the "whoops!" moments, that's for sure!