I don't put actual windows in my coop...Just hardware cloth covered holes with wooden flaps I can close up if the weather is terrible...
My main coop is the top half of a large building that has 3 windows..One of them was broken, so we removed the panes and just covered the whole thing in hardware cloth, and no issues with that even during winter...It is my ventilation. Putting actual windows in a coop seems odd to me...When the hole with flap is so much easier and cost effective. And the fact that unless you have some really nasty weather the chickens prefer the windows open anyway.
The higher up you can put your ventilation the better. I was tossing around the idea of using one of those metal barn shed things as an extra coop and just cutting out a strip of roofing along the middle seem and sort of steepling it up a little higher so there would be ventilation...but then we realized we could afford more space if we built it ourselves...so we're going to have holes with flaps all around...Lol. I still need to add some extra ventilation to the duck coop. We left a gap all around the top under the roof that we then filled in with hardware cloth, but it still seems like it would be stuffy in the back of the coop...since only the front is raised in such a way...
I figure a large rectangle on either side should do it.