Welcome to Tom's Forum!
I have the same MOBO, you have (2) choices SLI or single GPU: 1. 2nd PCIe x1 (underneath SABERTOOTH X79 on MOBO), or bottom dark brown PCIe x16 (x8 mode).
I have SLI and my preference is the bottom dark brown PCIe x16 slot. The (2) tan PCIe x16 are best for GPU's, and I agree not to needlessly block the GPU's intake.