I believe that your PCI-E 3.0 lanes (16) would be hardwired to the X16 slot. The chipset (H81) supports 6 additional PCI-E 2.0 lanes. It's from the chipset that the X1 slot would get it's lane.
That said, even if your graphics card only got 8 lanes, its been shown that a graphics card doesn't show any appreciable degradation in performance down to 4 lanes.
If you want to be certain, download GPU-Z and you'll see PCI-E Bus Interface. Sometimes what's displayed here will be less than you expect, in this case, just hit the question mark icon and then Start Render Test and then recheck the PCI-E Bus Interface.