I was installing an Enermax ETS T-40 heatsink onto an i5-2500k cpu. The instructions were really confusing because the diagram was incorrectly drawn and the backplate kept coming out crooked when I installed it vertically. I ended up installing the backplate on the motherboard in a horizontal position. Everything fits fine, the heatsink and fan, etc. Will it be a problem if I leave the backplate in a horizontal position?
What mbod? Some MBODs have north bridge chips that get their cooling from the cpu fan. Just make sure that your cpu fan is colling everything it's supposed to. Other than that, I don't see any problem with a vertical or horizontal choice.
Does that mean your fan is in a horizontal position? I don't think the back plate's position makes much of a difference, as long as the fan can be placed so the air flow is pointing in the direction you want. If the fan is not going with the flow of the case, then you will lose a couple of degrees of cooling in the CPU, and possibly, as terry said, no northbridge cooling.