Why don't you post in Off-topic if this isn't about Linux tech support??
Microsoft said that Win98 should install before you installed Win2k on it. Because Win2K support multiple booting ( and I am not sure about Win98 will support it ), you might have some trouble getting Win2k boot loader ( NTLDR ) seeing from BIOS once you installed Win98 loader.
I guess also if you save boot.ini and ntldr from your first HDD ( no matter where you installed your WIn2K, those two files will go to Primary partition of primary HDD ) to floppy, and then re-copy it after you install Win98, that might as well work ( this is from the guess. I've no hands on with this type of set up. )
So my suggesting is that save all your data off of Win2K and try to install Win98. Expect to loose Win2K if it is not work though.