It sounds as though, when you first installed WHS, your one and only disk wasn't connected to your 'disk 0' motherboard connection. It now really depends on your BIOS. If you can choose which disk to boot from, I would be surprised, most systems only let you choose Disk-DVD-Floppy etc.
If you have any disk duplication software, you might be able to transfer your OS to your Primary IDE, it could be worth trying, otherwise I'm afraid a re-installation onto the correct disk will be required.
Colin