I would use the fan as a rear exhaust.
Mainly it is to draw the front intake cooling air past the cpu cooler and out the back.
A top exhaust will tend to divert the cooling stream straight up and not let it get to the cou cooler.
I like the positive pressure aspect of having all of the cooling air intake come from one source.
In time all of it will exit the case somewhere, taking component heat with it.
If that single source is filtered, your parts will stay cleaner.
A second exit fan will tend to draw in unfiltered air from adjacent openings.
With that in mind, the difference is so small, it really wouldn't matter... that's too neutral an answer though, so I'll add:
-If your cpu cooler is a tower model: rear exhaust.
-If your cpu cooler is a top-down model: top exhaust.