First, back up your data and assemble the CDs with your MB and expansion card/peripheral drivers and your OS.
Then boot to a floppy or CD (use your BIOS setup to make the CDROM and/or floppy bot before the hard drive). With a floppy, first use FDISK to remove all partitions on the HD, then make new partitions. Reboot to the floppy again and FORMAT the new partitions.
If you boot to your OS CD, you can use FDISK (Win9x) or the NT disk administration tools to remove and replace your existing partitions and prepare (format) them. Unless you need to access an NT-OS partition from a DOS 7.x bootup, use NTFS with WinNT, 2K, or XP. Otherwise, and in Win9x, use FAT32. Name your partitions for convenience.