If you must have a roof mounted air conditioner, it should be as close to the front as reasonably possible. If you've ever seen wind tunnel smoke trails over a vehicle, the windshield clearly redirects the airflow primarily over the vehicle, increasing air pressure over the top of a tall van more than you can imagine! However, it takes a few feet for most of the redirected air to flow back to the roof surface, creating a bit of a bubble of relatively lower air pressure near the front of the van roof... where you should place a rooftop air, if you must.
In our experience, we now know the roof is the worst place to install things that obstruct airflow... we believe decreasing MPG up to 6-7%, depending on size & placement.