Using the second PCIe x16 slot will knock down the primary slot to x8 even if you are only using it at x1 or x4 speeds, but it won't cause anything like ESATA or USB to stop working. In fact, with your video card, you likely won't see any performance decrease even with the primary slot running at x8 speeds. This is an older(ish) article, but it shows the difference between running cards similar in performance to your in both x8 and x16 modes (just ignore all the SLI/Crossfire stuff): The Difference Between PCIe x8 And x16
. So at most, you might see a ~2 FPS drop while gaming.