Using 2 Hard Drives, how to separate files Options

[don says mac]

i'm sure that most people have somewhat the same set up as i do, in that i have one 'boot' drive (40gig wd) for my applications and another 'capture' drive (160gig wd) for all my saved files (music, videos, pics, documents etc...). this is in case my boot drive gets corrupted, all my work is safe on another drive.

so i just cleared my drives and installed panther on both. when i put all my music files and my pics back on to my capture drive, it seems that it duplicates everthing onto the boot drive to access it. i'm having trouble telling my mac that all my files are coming from my capture. panther really wants to access everything from the boot. (i.e. if i have an mp3 on my capture and play it in itunes, it will remain on my capture and a file will be created in the itunes music folder on my boot, even though i've changed the directory in my itunes preferences). i don't remember this happening with jaguar. can anyone off some advice?

thanks,
d