hey -not much help to you prob, but this is how i save my stuff:
250meg zip disks, partitioned A-E, (i've got about 30)
save all sequence and songs (not forgetting to name it something completely obscure and irrelavent, so when you are looking for something you can never find it!)
change the name of all sounds individually in trim (so when you do an APS save you dont overwrite previous sounds on that partition that may have the same name)
save all programs and sounds (again name it something that gives no clues as to what it is -i.e #kqjab___12c).
i save and resave as i'm working -constantly updating as im scared that my mpc will crash, have an SCSI error, or the electricity meter runs out and i get a power cut.
once i'm reasonably happy with a song i remove all unecessary data and resave as crunched-a-down version as possible onto another partition or zip disk. i have multiple saves of the same song scattered over many zip disks at various stages -better safe than sorry -i've hade to remake complete songs because i've not been bothered to save and my mpc crashes.
my method is totally inefficient and i'm completely unorganised, but it (kind of) works for me.
p.s never actually write on the disk what is on there, that would make thigs too easy!!!