Like Ironsounds said, the fans that come with the EVO have an arrow telling you which direction they blow. I think the CM Megaflows do too.
RE the CPU cooler orientation: what matters most is the overall airflow picture. If you're intaking from the front, and exhausting from the rear, it might make more sense to have your CPU cooler oriented vertically (facing back and front), so that the fan(s) on it will match the direction of overall airflow in the case. It wouldn't make much sense to intake from the front of case, exhaust from the rear, yet mount your CPU cooler so its blowing the opposite way. Perpendicular is probably okay, but if you don't have a top vent, you might be creating dead spots.\
EDIT: I should add, if you "rotate" the CPU cooler 90 degrees, the fan(s) might be wide enough to overlap the RAM slots somewhat. Make sure that's not an issue for you (either using low profile RAM, or only two of the slots).
Make sense?