I am also interested in the answer to this question. I guess if this is possible it should be done with somethig like PCIe extender.
I have a bad experience with old MBs. Recently bought Connect3d ATI HD5570 (for having hdmi output to TV on my old PC), inserted the card and nothing happened - still the built in VGA card was working. BIOS options were fine - use PCI Express Video card.
So I've updated the BIOS of my old ASROCK MB and after this the ATI turned on. I've installed Windows XP without problems, restarted the machine and again ...
the built in video VGA was up and running again and no VGA signal into output from the ATI card. Checked the BIOS options - PCI Express was selected.
And this continued happening at random intervals - Every time I turned on the computer either built-in card is on or pci express is on without a way to control it. So I gave up.
Any ideas ? I guess to buy a new MB
Mine is ASROCK ConRoe1333-D667 running the latest BIOS