1st. I don't think there is a PCI 16x, PCI is 1x (I think) and PCI-e is 16x. (well sometimes 8x if used in SLI, depends on the mobo)
But go to the bios and see if u can disable the onboard vid card, or something similar. And u always need to install the vid card drivers, always! (well u can run the card without the drivers, but then it's not going to perform even close to what it should)