I had a similar problem. Both of my hard drives sit on the CMD ATA/66 controller ports on my Asus CUBX. The upshot is that the Win2K installation can't handle it properly and dies. And the F6 thing to import drivers during the process doesn't work very reliably (at least with my set up).
Try this (it's what I did).
Open up and reconfigure your system temporarily. Move the new drive to one of your standard IDE ports. You'll need to make sure your CD-ROM drive is on one of them too (i.e. - have both hard drives as master on the two standard IDE ports with the CD-ROM as slave on one of them).
OK once you've done that, go through the Win2K installation procedure. It should install quite happily onto the second drive.
Once it's up and running, install the drivers for your PCI IDE card and make sure that Windows 2000 can see the extra IDE channels.
Shut down and put all the hardware back how you want it.
Boot, and 2K should come up OK.