Did the case come with a bunch of riser screws like this: http://www.heatonresearch.com/images/article/21/ch3fig4... or similar? If it did then you need to screw them in to the holes on the inside of the case that line up with the screw holes of your motherboard (there should be 9). It is also possible that the case has built in risers (it would be an elevated part of the case in 9 places with a hole a screw can fit in).
Once that is done (if you had to do it) put the motherboard's I/O shield in to the case (it came with the mobo, not the case).
The next step is to put the mobo in to the case and screw it in place. After that all the other instructions for the cables that came with the case will be in your mobo's manual.