the vp6 has had problems booting from some specific models of scsi cards from adaptec, specifically the 29160 and 39160 line of cards. more info
here. i don't know if there's a bios fix for this, but there's the workaround.
is there a particular reason you're going raid 1? if you're just going to store a lot of mp3's mostly, i would just leave them in normal configuration and save that 30 gigs.
if you do plan on booting to 3 different platforms, you might need some 3rd party software to handle that for you, or if you do boot from scsi, you can change the bootup id and hence switch to whatever drives you want to boot up to, given that your first bootup device is scsi in your mainboard's bios. win2k should detect win98 so they can coexist on the same drive, just as long as you install win98 first and then do a clean install of win2k. win2k can be on any drive you want, just as long as it has a footprint on the boot partition of your bootup drive. if you want to install linux, i guess you could put that on your eide drives if you wanted to and switch the bootup device in your bios from scsi to eide. that's kind of hoky though.
for simplicity's sake, i would just install linux on one scsi drive and win2k/win98 on the other. this way, you can just change the bootup id in the scsi bios and startup to whatever drive and hence the os of your choice. on the win98/win2k disk, win2k will make an operating system menu and you just select which os you want to go into. the thing i like about booting to os' this way is that it makes them independent of one another, so you could take out one drive and still have linux or windows. or if one operating system goes bad, it doesn't take your ability to boot if it does corrupt the boot sector of a disk because there are 2, one on each scsi drive.
if you want to make the operating systems ultra-independent of one another, you could install one operating system on the eide disks, and one on each scsi disk. the way you would have to boot to any operating system in this configuration is that you would have to change the bootup id in the scsi bios to bootup to an os on the scsi drive of your choice. if you wanted to boot to the eide drive, you have to change it in the mainboard bios and change the boot order to give eide priority over scsi. sounds complicated, but i like this approach because if you hose win98, win2k is still good to go, and vice versa. this helps with backing up data on a hosed os drive since you might not be able to access the files. i would definitely make the windows disks fat based, so you can read files across the different platforms. i'm not familiar with linux, but i think it can use fat as well. whew! that was a long post. hope this helps you out.