I also would like to know the answer to this.
Just bought a sabretooth z77 but am still using my gtx560
Not sure if I should have it set at x1 or x4.
From what I understand(which isnt much) you can have it set at x4 assuming certain ports(not sure which) are not being used by other devices.
The PCIe 'Express' 2.0 x16_3' has nothing at all to do with the GPU's PCIe 3.0 slots so x1 vs x4 won't do a thing. The 16 lanes of PCIe 3.0 are a direct path to the Ivy Bridge CPU, and under a Sandy Bridge are running @ PCIe 2.0.
Changing PCIe Express 2.0 x16_3 x1 vs x3 = No Change to GPU(s).