I think you would put your Win03 server disk in your CD rom, and boot from there. You can either do this in the bios by making it the first boot device, or you may have a boot option at start up.
Either way, booting from the cd should allow you to format and install in one operation. (Obviously, you will delete everything on the disk).
Edit: If you parititioned using PM or something, you can format your "C" drive there and make it "active" and then boot into "C" and install your OS.
Edit 2: Lets slow down a second... First, Each OS stands alone on its own parition. You need a "blank" formatted partiton to load your OS on. You cannot get there though another OS. Think of your partition as a mini hdd standing alone. Treat it as such. Then when you are done, you can choose which OS to boot into, by picking and choosing which one to make "active" for any given boot - up.