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The problem is that Win-98 will always write certian files to the C drive even if you choose to install it into another partition. It will overwrite the MBR with a pointer to boot Io.sys and msdos.sys leaving you unable to boot into 2000.
Thats why 98 should be installed first to be able to use the win-2000 boot loader to choose between the two OS's.
It is possible to install 98 after 2000 or XP but it's a little more complex because you have to generate a win-98 boot.bin that will be recognized by the NT boot loader.
khauyeung made an excellent post with the procedure to do this but I'm unable to find it now, but you may want to search his posts for it.
Only other way to do it without re-installing is to use a boot manager like boot magic that will hide two primary partitions from each other but you won't be able to access those partitions from the other OS.
Best of luck,
Dave
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