The IO plate on the case comes off. Your motherboard will come with a IO plate that is matched just for that motherboard. You remove the one that comes with the case and insert the one that comes with the motherboard. Each motherboard comes with one specific for that board.
As for the GPU fitting I can't really comment on that because I have not ever used nor would I ever use any case smaller than a Full Tower. And I could not find anyone on Newegg using that case with a large full length GPU sorry. Mayby some one else can chime in on that.
As for it working on the motherboard that should be no problem.