I booted from the Win2K disk and installed the OS,
Somewhere during that procedure, very early on, were you given a screen that showed you the partitions on the hard disk, asking you where you wanted to installe Windows 2000?
The correct thing to do on that screen is to select the existing partitions and press the D key (I think, I don't recall exactly) to delete the partitions. Then there is nothing left on the hard disks and it just says "empty space" or something like that in the list of partitions.
Then you install Windows to the empty partition. It asks you how you want it formatted (FAT or NTFS) and you say NTFS.
That's the proper way to install Windows 2000 from scratch. No need to use a DOS floppy or FDISK or anything, because it's all built-in to the Win2K installer program.