Is the fan meant to cool the chickens themselves during the hottest part of the day, or cool the coop when the outdoor air is cooler than indoor?
If it's meant for the chickens at 4 p.m. type of thing, it needs to be blowing directly on the chickens.
If it's meant to run only when the outdoor air is cooler than the indoor air, and intended to bring indoor temperatures down as quickly as possible in the evening, then I would strongly suggest you have the fan blowing IN. This will minimize the amount of dust that gets in to clog the fan and decrease its performance and cause electrical hazards.
Another electrical appliance that would probably do an even better job increasing the ventilation in your coop would be a reciprocating saw. Honest. If you are in a hot climate and have only two windows and a door, you would be well ahead by going and cutting another large opening in the coop -- like as large as you can manage without compromising structural integrity. Studs can cross it, so you can just cut a hole of siding out and put up hardwarecloth and trim if you want. Save the piece you cut out to bolt back on to close it up for wintertime if you think you'll need to.
Good luck, have fun,
Pat