On many older compaq's, you have to confirm system changes in the BIOS. When you see a flashing cursor in the upper-right-hand corner of your screen, press F10, and you can enter your BIOS. Make sure your system is set up to detect drives on both controllers. Save your settings, and exit. Hopefully you'll be all set after this.
If you press F10 and you CAN'T get into your BIOS, then you'll have to download the setup-utility floppies from the Compaq web-site to enter your BIOS program.
Hope this helps-
Joshua Van Berkum