On the C2SBC-Q motherboard with Matrox VGA card fitted, though I have disabled the on-board VGA from the BIOS, when the system is powered on from cold start, it defaults back to the on-board VGA. I have looked at the manual, but there is no jumper to disable the VGA.
You cannot disable the on-board video, but you can change the Default Primary Video Adapter on the BIOS menu.