I feel like this is a simple question, but I should ask it just in case (don't want to take a any chances). When I place my motherboard over my case I see which holes I will screw them into, but 4 of those holes seem to be raised (It's best seen on the newegg link I gave, the sixth image[the interior]). Should I still put the hexagonal screws in those? Or just leave those 4 holes alone and put the hexagonal screws in the rest?
The brass stand-offs (hexagonal screws, as you put it) are sent with all motherboards because 99% of the time the mobo's are being installed into cases w/o the raised mount holes.
To answer your question, no, don't use the ones that came with your motherboard, if you do, the motherboard will not line up with the I/O space. Mount your mobo directly into the case; do not use the stand offs.