Actually a cupola can be great to get rid of bad air. Ammonia is lighter than air and will rise to the top. Warm air is lighter than cool air so it will rise to the top too. In the wintertime a cupola may be plenty to get rid of bad air. Part of that is how it is built, how many and what size the openings are. The more vertical difference in the openings the more air exchange you can get. Other openings above where they roost is a good idea in winter, but a cupola is a great start. Just make sure it is strong enough so a raccoon can’t rip it apart and things can’t limb in through the openings.
In the summer you need an opening lower down to let in cool air. A pop door, a window at or below roost height, or another vent down low are all good. In the heat, it’s next to impossible to have too much. It helps too to have at least one of the openings on the north side or in a shaded area so the air is cooler.