Are you sure you have the Commander Pro and not the RGB Fan Lighting Hub? IIRC, that case comes with SP-RGB fans and a Lighting Hub with a push-button controller, not a Commander Pro.
As for plugging this in to your motherboard RGB header, that's not going to work. First, they don't fit. If, however, you do manage to mangle it on to the connector (and there are those that have) most of the motherboard headers are 12V and the Corsair RGB LEDs are 5V ... so you'll blow the RGB out.