Holy crap, I think I'm just an idiot. The 2 prongs are for the fact that the card takes up TWO SLOTS. I don't recall it aligning that way though. I was able to put the new card into the PCIe 16 slot, but the bracket prongs didn't seem to be aligned...
Jeez. I will try again when I get back into the case.
(Again, just my first time to do some DIY stuff...sorry!