I like those kits that have integral windows and windshields in clear fuselage. Yes, it can be difficult masking, but often windshields do not fit very well, and puttying and sanding the putty can be harder than masking. Use a good masking tape, such as that from Tamiya. I mask both inside and out before applying any paint. Then I paint the inside. Yes, this will prevent treating the seams on the inside, but these are usually not that visible through windshield and windows. Then I remove the masking from the inside.
Then I assemble, and eventually paint the outside.
As far as the masking itself, usually there are embossed lines representing the outside of windshield and windows, and I mask exterior first. I then place masking on interior of windshield and windows to match the masking on the outside.