According to your user manual, page 2-15, inserting your vid cards in slots 1 & 3 should auto-result in 16-16 operation. A quick scan of the bios section of your manual did not show me a related bios setting, so it should all happen automatically.
Are you *certain* you are using slots 1 and 3? Please note that slot #3 may NOT be the third PCIE slot. The first physical slot is almost certainly the real "Slot 1", but check the identifier on the board near the socket and find the slot labelled "PCIe 2.0 x16_3" or something similar.