Richard,
I built a Sikorsky S-39 years ago for R/C from plans in RC Modeler.
I set mine up exactly the same way a door glass would fit into a door.
I used two layers of balsa. One layer was the outer fuselage skin. The second was the frame the clear plastic sat on placed behind the fuselage skin.
Then, I made a frame of thin 1/64 ply with a glass layer, and carefully epoxied them in place over the clear plastic.
You could use CA but then heat won't allow you to easily remove any window for repair or a redo.
Sounds like a good deal of work doesn't it. Well it is.
Me being like I am, the results were worth it.
Unfortunately, the model has been taken apart and striped for a redo. I couldn't save the old frames, but here are the new ones I made a few years ago.
I pulled the model out and took these photos just for you, I hope they help.
See what others come up with.
CB