A couple of ideas.
1. If you want to take advantage of the larger partition size available with Win98, you might also want to partition first. Win95 had that 2 gig limit. This way you could use your entire drive as one partition. Not saying you should do this but it is a possibility.
2. If there is any data you want to keep, and don't care about the partition size, you don't necessarily need to reformat to effectively have a clean install. Just boot to DOS and rename or delete the current Windows and Program Files directory. Then install like you normally would.
3. In all cases, it might be a good idea to backup any critical data or configurations first.