If you booted from the Windows 2000 CD to perform your installation, you might have noticed that one screen allowed you to set up your partitions before actually installing. If that is indeed what you did, just boot from CD again, when you reach this point, delete all partitions from your proposed system disk (just highlight and press D, but all required keypresses are indicated, as usual, at the bottom of the screen).
When you see no partitions remaining, don't bother creating any, just press "I" to proceed with the Install; as a slight time-saver, the installer will create a single partition (using the whole hard disk) itself - the only input you'll need to give is to choose FAT32 or NTFS, and sometimes, whether or not you just want to Quick Format (but you may not see that if you completely removed all previous partitions).
That should do the trick. If for some reason you can't do that, simply find a Windows 98 boot disk (or something similar), and use FDISK to remove the partitions (should work, but i don't know the size of your partitions, FDISK may not see them if too large), then proceed with your install.
As one final note, if you have multiple hard disks installed, it might be worth disconnecting them just to be on the safe side (the partitioning tool asks for confirmation on delete, but you never know, mistakes can be made!)
Good luck with your install.