I tried two methods with the windows.
First of all, the plexi glass I used for windows came with a tight protective film both sides.
Secondly, I paint major parts off-build and assemble completed parts (and clean the seam areas afterwards).
1. installed a window, painted (or varnished in my case) over, removed the protective film. To make sure I also used liquid mask around the edge of the window.
2. paint and varnish everything without windows and then cut and install the windows by using canopy glue. CG can be applied on painted surfaces and spills are easy to rub off.
I have decided to go with method 2.
I liked Andy’s choice of installing windows inside the frame so much that I’m now following his suite - albeit in my clumsy fashion
He uses 2mm plexi, I use 1mm, advantage being that for cutting, I can use a pair of scissors.
I hope I’m being helpful!