The answer to the "how do I disable the integrated VGA" is: You don't. The integrated pseudo-AGP device will coexist with the added PCI VGA. Proper BIOSes should let you set the preference for the boot output device to PCI or AGP, and that's it.
There are plenty of boards which, thanks to BIOS fsckups, don't do that right. If you got one of those, you're lost.