I think you might have to install 98 on youc drive. There is a way around it though. unplug the drive with 2000 on it and just install 98 on the other drive.
Is 2000 NTFS? if it is then you can leave it like it is. If it isn't you might have to put the 2000 drive as slave and change drive boot order in bios. If you leave it like it is and 2000 is fat32 98 might try to write to the drive when it boots up. (I'm not really sure though.
I have XP on a raid controller (Ide 3) and win98 and a storage drive as master and slave and I haven't had any problems at all.
You might try
www.ntfaq.com and see if there is anything there that would help you.
Good luck, I wish I was more help,.
Will