My coop was converted from an old rabbit cage that was made with a wood frame with hardware cloth nailed on all sides, the top and bottom. When I remodeled it for our girls, plywood was screwed over the floor from the inside, and over the walls from the outside, so the wall wire is exposed on the inside of the coop against the plywood.
I measured and cut out the plywood sections for the walls so they would fit precisely and overlap at the corners. For windows and ventilation I made cutouts in the plywood pieces before they were screwed onto the wall framing. They are whatever size I wanted and at whatever locations I wanted--some large, some small, some high, some low--for varying weather conditions and air flow patterns. I made my cuts fairly precisely using a circular saw for the long runs (making a 'plunge' cut) and a jig saw at the corners, so the openings are fairly neat. Then, as I cut the various pieces out I labeled them and the opening so I knew which piece went where and how it was oriented. After I had all of my cutouts done, I went ahead and screwed my wall panels onto the framing. (You can nail or screw them. I prefer screws.) So now you have a coop with plywood walls and window cutouts but no windows.
Next, I scrounged some pieces of Mulehyde membrane roofing material--that rubberized, thick material used on flat roofs--from a generous roofing contractor. I then laid out the membrane on a table and placed each window cutout on the membrane so that there was a one-inch border of roofing material LARGER than the piece of plywood cutout. I marked that one-inch border with a pencil, then cut the membrane with a utility knife. Then I used short galvanized screws and screwed the membrane to the outside of the plywood piece being careful to leave my labeling marks visible (remember them because they help with getting a good fit for the window "shutter"). Usually I placed one screw near each corner and one or two on the top and bottom center to keep the membrane firmly and smoothly attached to the plywood. Next, I was ready to 'install' the window shutters.
I cut a strip of pressure-treated plywood about 3/4 inch wide by the exact length of the membrane on the exterior of the shutter. You can also use a wood strip or even a metal strip. I had extra plywood scrap so I used that. It's best if it's pressure-treated or weather resistant because it's on the exterior of the coop. I pre-drilled three or four screws into the plywood strip with the points just shy of breaking through the plywood. It's important that the screw length is short enough that you don't have a sharp point penetrating the side wall of the coop--a potential injury to your birds. (The good news is there are MANY different lengths of screws available) Then I placed the numbered piece in its corresponding window opening (in the same orientation as it was cut OUT of the opening). The piece will fit perfectly into the opening because it's about 3/16" smaller than the opening due to the saw kerfs (cut path of the blade). Using 'feel' I tried to center the plywood so it was not touching the sides, bottom, or top of the cutout opening. Once I had it right, I laid the 3/4-inch plywood strip over the top edge of the membrane (that extends beyond the plywood by an inch) and screwed in the screws I had pre-drilled. The plywood strip held the membrane tightly against the outer plywood panel without it bunching up.
After the screws are in place in the strip over the top border of the membrane you should have a fully protected window. The sides and bottom of the membrane overlap the edges of the opening by about an inch, giving extra protection from driving rain, snow, or cold air. If you have fitted the window/shutter correctly you should be able to easily open it by lifting it by the bottom lip of the membrane border. You now have a fully-covered window opening with a flexible, weather-proof covering.
All you need now is a way to keep it open or closed. I used one screw driven through the outer membrane and into the plywood shutter about a half an inch above the bottom center of the shutter. Then I wrapped a good length of galvanized wire around that screw between the screw head and the membrane. Next, I screwed another screw into the plywood coop wall above the window about two inches. To keep the window open I simply raise the bottom using the wire attached to the screw, then wrap the loose end of the wire strand around the screw I just placed into the coop wall above the window. If you leave plenty of wire you can open the window wide or you can just barely 'crack' it.
To close the window tightly (as in the dead of winter) just drive another screw in the coop wall just below the lower membrane border/flap and wrap the loose end of the wire around it to keep it closed.
Using this method, I have been able to adjust the opening of the windows to WIDE OPEN when it's blazing hot and they need more ventilation OR I can have them halfway or two-thirds open if it looks like we are going to get some wind-driven rain.
The good thing about this method is that you don't have to buy windows or hinges. You already have the plywood for the coop walls and you have to cut the openings anyway, so you are using "waste" material that would otherwise get thrown out. The membrane scraps, even if you buy them, are not very expensive. The screws are probably the costliest item.
I hope this is helpful.
If it's too complicated or I did not explain it clearly enough, let me know and I will try to post pics.