The 2000 disk probably has its partion(s) formatted using NTFS - a file system that 98 can't read or format. However, 98 should be able to delete this partition. You say that you are able to boot into 98 with the 2000 disk as a slave. You should be able to do this so shouldn't need to make a boot floppy. So from 98 bring up a dos prompt and run FDISK.
You should be able to select your slave drive and delete the NTFS partition - then create a new partition this time formatted using FAT32.
Now I can't remember how FDISK menus work - so you can't need to give exact instructions. But please be VERY CAREFUL - if you accidentally delete your Win 98 partition you won't be able to get it back!