Hey there.
The 4-pin molex connector is to provide additional power to the second PCIe port if you had a device that needs it, which, chances are, you don't. It's not for the x16 slot where your GPU would go.
The 8-pin socket on the top left corner is actually where your 12v 4 pin connector goes. If you look, the notch is positioned such that you you can snap into place and leave the remaining plugs empty. I discovered this using an Antec Earthwatts 380 with the board for a while.