Some bios's will disable the onboard graphics card automatically.
There are 3 types of drivers for ATi cards:
Official Catalyst
DNA
Omega
Also there are different versions, the latest being 4.4.
The Nvidia 6800 did improve Directx 9 performance, but in some directx 9 tests it was not rendering pictures very well, but i would put that down to beta drivers it is using right now. The X800 actually broke the 3DMark03 world record recently, by getting just over 15k, and the 6800 touched 12k (both cards at stock speed). You may need to upgrade your PSU for a 6800, also you will lose a PCI slot for it aswell. Either one you choose you will be very happy with your choice. Assuming you want to shell out lots of money for those top end cards. If you look around at the FX and Radeon range now you will find the prices are lower than what they used to be because of the new cards that were released.
Also currently ATi cards are 4-5% cheaper right now, so the difference in price is minimal.