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 ...
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 ...
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