you'll probably need a boot disk with some generic data on it. Like f-disk and a config. sys file to acknowledge the CD drive... Otherwise, when you wipe your drive, you have nothing when you boot. You won't be able to access anything but the little floppy and the hard disc. Newer versions of windows have fixed this, but 98 is old enough to where you still need boot disks.
Not hard though, just think of what you'll need before you actually do it, that will same some grief later.