Been a while since I did this.
If you try to boot the 98 machine with a 2000 disc in it, it may well not boot at all, as it may get upset with the format of the 2000 disc.
So, to avoid that sort of hassle, make yourself a boot floppy, and then add the FDISK ( or is that FDISC) and FORMAT tasks (the .exe files)
Attach the 2000 disc to the machine as a secondary disc, not a primary device, then make sure that the BIOS can see the device, so that it can be got at within the operating system.
Boot from the floppy, get to the DOS prompt, and then run an FDISK on the 2000 drive. Grea care to avoid the "live" drive, FDISK is not particularly user friendly, and the interface is more than cranky and old!
After the FDISK, you will have to reboot to make the disc visible to the OS, boot from the floppy again, as it's quicker and avoids possible hassles, and format the drive (with GREAT care that you don't by mistake format the C: drive!!!)
Once that's done, it should all be present and correct.
There's probably a quicker way to do this with something like partition magic or similar, but if you don't have them it costs, this way should work without spending any more money
Hope this helps