Ok so the basic still apply. You want the pump to be fully saturated with water. You also don't want air in the block. Air doesn't move heat. So...
if you top mount it put the pump near the top of the loop which is where the air is going to sit. The plus is the pump isn't in the center it's off the the the side. All that need to be done is to mount the cooler slightly tilted. Just put a couple washers between the aio and the case on the side with pump.
Other options is front mount as long block is lower than the top of the rad. Tubs down/pump down would be best.