i would suggest you keep both file systems as FAT32 to begin with, then later if you want to get NTFS for win2k you can convert. you can convert fat to ntfs, but not the other way around.
also, i would suggest doing as deadeye suggested and making three partitions, a 2gb, 4gb, and 54gb. install 98 on the 2gb, win2k on the 4gb, then all of your programs and stuff on the 54gb. and keep the 54giger FAT32.