You should have a windows boot floppy (with fdisk on it), first.
Then you should check your BIOS (hold DEL while rebooting probably) to see if you can boot from CD. If not, get hold of a CD Driver floppy before you go on.
If you have done these things, then put the win98 boot floppy in the drive and reboot. Run fdisk off the floppy to clear all partitions on your hard drive (assuming you don't mind losing any data) and then try putting the CD in and running setup.
Win98 has a very hard time installing on a drive that has had linux on it though (at least in my experience) so be patient. If it doesn't work, just keep trying.
Once you've got it re-installed, I'd go for a dual-boot system
Best of both worlds!