You may be pointing to the wrong device. Some mobos have many on board logical connections an lump them into raid or sata. What mobo are you using? The boot priority is auto negotiating, so you really don't need to configure this.
When I go into disk management, my new HD is showing up as the boot drive with a partition on my old HD as the system. Do I need to get the new HD to have both? :? (no idea why I'm having all this trouble though, I've replaced HD's plenty of times before, though I suppose this is my first SATA drive)