what board do u have? steps:
1. prepare the board, remove every hardware from it. if u have i7, remove the stock backplate. with the mugen 2 backplate i think spacers are needed (see the manual).
2. put the mugen upside down (the base to be up) and put some thermal paste.
3. now take the board and put it on the cooler. make sure u put it in the needed place, the wholes need to line up.
4. put the backplate on the motherboard, and put the screws. close the screws in order 1-3-2-4 (screw in the first, then the 3rd, so on.. but not all the way, just a few rotations) at the end all 4 screws should be put in all the way, nice and strong.
5. now just put the whole board+cooler back in the case and add the rest of hardware.
i also advice u to...