most cases do two tricks with muilt port usb. 1. they splice two or more wires onto the same usb pins. 2. they use a small daughter card in the case or controler that goes from one usb port to two or three and a card reader.
I think you are good to go, from the description "Both USB3.0 ports are connected via a 19-pin motherboard connecter and offer an alternative USB2.0 connecter to ensure backwards compatibility with older motherboards." I am assuming that means a single header plug.