I only realised the same thing last night, the corsair fan connector that cones with the case cant be used on the motherboard, and vice versa so aftermarket won't fit in the fan controller.
Could of done with this reply last week. Thanks all the same.
Sucks, but at least you know how to move forward with this now. Either mod the corsair fans, or use aftermarket fans on an aftermarket controller or directly on the mobo headers.