Drapes,
Set the W98 disc as Master (C:/) and W2K as slave (D:/).
Computer should now start as a W98 machine. select my computer, and right click on d:/ drive. Select format. should ask you to verify as formatting will erase everything. select yes , and away it should go.
Should that fail for some reason you could delete everything on the hard drive. and try again. If this still fails, reboot using your W98 boot disk.
Now you type in fdisk at the promt. select the second drive, remove/ delete partitions. Now recreate the partition/s you want. Exit fdisk, and enter format D:/. this will reset the HD as a dos / fat32 drive.
remove boot disk and restart the computer, you should now be able to see a blank hard drive ready for you to do that which you will.
Hope this works for you.