OK, pop in a Windows 98 bookdisk... it will then ask u if you want to boot with CD-rom support, choose Yes... Then it will load all the DOS functions you need into a RAM drive...
After everything is done and you get the DOS prompt, you can load fdisk and format from the RAM drive to do what you want (repartition, format, etc)... After you are done, just pop in your win98 CD, go to the CD drive and type setup to start re-install Windows 98...