I build most of mine with the canopies open, and so far they have all be sliding canopies so I don't worry about what the inside canopy lines look like. In fact I had never even though about the inside canopy lines. rjkplasticmod's idea is a very good one.
To answer your question, I paint the canopy lines on the outside and always mask and airbrush them. I just can't keep the lines straight enough to paint them by hand without masking, and if I'm going to mask them I might as well just airbrush them.