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)
I suggest to avoid compalitly issues, and conflicts with onboard GPU, and off board that you disable it manually after you've installed your GPU, remember to uninstall the onboard drivers as well as those can create conflicts with the system and cause a unstable OS.