OK, the cables running from the front panel USB 3 ports say USB 3 on them. They both seem to link into the same female connector which then plugs into the male port on the board. (on the left of your picture)
From what it sounds like you are saying I somehow need to change the connector on the wires and plug into the dark blue female port between the ATX connector and next to the 2 lighter blue and grey USB ports on the board (on the bottom of your picture)?