I too was going to use the windows and fill round them, but when I offered them up you have the trim around the edge that sits proud, and the glass itself which actually sits recessed slightly, so very hard to make all that even, well for my limited skills anyway, so I just cut to size some 0.75mm styrene sheet panels and stuck them over, they are thin enough so you can barely tell they are there.
I also wanted to fill in the sunroof and side roof windows, however after having a bit of a play decided not to venture there, I will just end up making it look worse.