Turn on the computer and go into your computer's Setup (not the OS's). It's usually the F2 or Delete key. If you don't know which one just hit the Pause button to pause the screen to read, then the Spacebar to allow the system to resume. That way you can read thru all the bootup stuff.
When you get into your computer's Setup look for 'boot options'. Go in there and change the boot sequence to 1) Floppy, 2) CD-ROM, 3) Hard Drive, etc. That puts the CD before the harddrive.
Next put the 2000 CD in the CD drive and exit Setup.
Your machine will reboot and boot off the 2000 CD before the HD. Use 2000's Setup and on the 'Choose Installation location' screen select Delete partitions and to reformat the drive so you can do a clean install. When it prompts for Qualifying product (if you have the 2000 Upgrade) pop your '98 Disc in the CD ROM.
Now if you had your hard drive manufacturer's utility floppy you could boot off that, choose Diagnostics and 'Write 0s to the Drive' to get rid of that nasy worm/trojan you probably have on it that choked-off '98. If you do that be sure to hard power-off (flip off the power strip) at the end of the operation to dump RAM in order to exterminate the little bug. It won't 'hurt' anything because the drive is totally wiped. It also resets bad sectors so it's my preferred method for wiping a HD.
BTW 2000 has protected memory and file systems so you don't have to worry much about malware getting on the drives as long as your boot media is clean. If you boot with an infected floppy or CD in a drive the bug will get loaded into the OS and you'll have to wipe the drive again.