Ideally you want the cooler mounted vertical, as in having the fan blow air from the front of the case to the rear so the rear exhaust fan can exhaust the warmer air out the case.
Having the cooler horizontal isn't a bad thing either, a couple of things to note though, make sure the fan is facing up and pulling air from the bottom of the case to the top of the case, having top mounted fans or at least vents to allow the warm air to escape will be a big help.
From my testing the temp difference between having the cooler vertical or horizontal is only a 2-3 degrees difference in CPU temps and that's with the hot running R9 290 in the case.