Does your motherboard come with a PCI card with USB 3.0 ports on it? That should have a cable that connects to the USB 3.0 connector on the motherboard.
Instead of having a cable run from the front panels, out the back of the case, then into this PCI card which connects to the motherboard, there is an alternative. Take the PCI bracket off the USB ports, and thread the connector end from behind the front panel through to the motherboard and plug it in. Pull the cable from the front panel back through the case to behind the front panel and plug it into one of the USB ports connected to the motherboard. Now you aren't using up PCI slots and don't have cables running through your case. Just tuck the cables neatly behind the front panel.