Hi Tim and welcome to the Gigabyte Forum.
If you mean the PCIEx16_2 then I don't see any reason why it shouldn't work. You can select it in the BIOS as the Primary Display Device. It is still the full x16 bus so no problem there and anyway it wouldn't use more that an x8 slot speed anyway.
I can't see why you realy need to drop the GPU down to that slot though as I have a similar board (UD7) and there is plenty of room for the watercooling as well as the graphics card and Silent Pipe Module.