Wells,
I went through all that. I have two hard drives. The original one was plugged into the Primary IDE port. I added a second drive and plugged it into the Secondary IDE port. It's an IBM Deskstar (40GB). I used the IBM utility, Disk Manager 2000) to copy the contents of the old drive to the new. But obviously I wanted to boot and run from the new drive. You might be able to switch the plugs around, but what I do is this: At boot up time, press your Delete key to get into the BIOS setup. In there, go to the boot sequence settings. You should see your legacy floppy drive, then your two hard drives in the list. Change the setting for your hard drives, so that booting up takes place from the new drive.
When boot up is complete, you will see that your NEW drive is now Drive C, and the old one will be Drive D (although W2000 assigns drive letters a little differently). The disk you boot from will always be drive C.
If you made your new disk a slave to the old one, did you check the jumper settings on the disk? I would recommend that you plug the new one into the Secondary IDE and make it the master there. Whatever you do, the jumper settings on both disks must reflect their true master/slave status.