I used plexi glass on all my windows. For all the windows it is cut to about the size of the hole with a one inch margin around the edges that over lap the wood. The front window is just one sheet on the inside. I figure the chickens don't care how it looks. I then lined the inside of the windows with sink sealant silicone. Drilled some holes larger than screws into the plexi glass and screwed the windows on to the door. I should have gotten washers to put under the screws though to deal with the pressure.
I ran out of silicone and it got rained on so the next time it dries off, I will take another tube of silicone and line the exterior side of the windows with a good helping of sink and fixture silicone sealant, so that water does not get trapped between the wood and the plastic and start to grow green. Reason I choose to use sink silicone, is that if I ever plan to dismantle it or need to replace a window, I can take off the screws and pop off the window.
In addition, the roofing panels have a layer of clear sink silicone surrounding the edges so if we get blowing rain, which does happen at time since it seems like it is always raining here, water does not seep in from the top. When it is next dry, and have attached the building to the floor, I will put a line of silicone along the bottom inside and bottom outside of the building where the walls meet the floor. This again, will have to wait till it is dry. I am glad I painted all edges and corners, as it would have shurly gotten water damage had it not been sealed.
Edit: If I were to do the floor again... I would have made it square with the size of the building so water does not seep in at the edges when water collects on the lip on the outside... I'm sure people who have made floors before would have known this. I made the floor 48 by 48, but the foot print of the building is really 48x 46.5 or so.