It doesn't matter. I put it that way so the exit barb was at the top left so there would be no chances of a bubble forming up towards the top. This is the way you used to have to mount the MCW6002 as well.
I really fancy getting one of those cases and am semi-intrested in watercooling in the future.. Where did you have the rad before, outside the case Im guessing? And could I stick the pump on the shelf kind of bit in the 5 inch drive bay?