Do you mean DOS or an NT command prompt? AFAIK, most BIOS updates are done in either DOS or GUI Windows. A command prompt only NT is a bit tricky, and not very useful anyway. A DOS booting USB stick ...
We all need to start from scratch sometimes and if you're building a new PC, chances are you'll need to learn how to make a bootable USB drive. This will enable you to boot your PC directly from a USB ...
Booting from the Win98 CD won't let you format from the command line, though you can fdisk. You'll have to boot from the CD to command line, fdisk at the prompt, then reboot (from the CD) and format ...