Windows are a point of contention for airliner modellers. Some people love them and others... don't. I fall on the "don't" side of the argument, so I fill the windows if they're left open. You may, of course, do the windows as you wish. Whichever way you do them won't be wrong. Just remember to paint the inside black if you do leave them open, otherwise the model will be spoiled by the white plastic being visible inside.
My rationale for using decals is that unless you're right up close, or looking at
exactly the right angle, airliner windows don't look clear anyway.
If there are clear inserts, I use them, then just putty up the gaps, Otherwise I glue in a strip of plastic card behind the windows and then apply putty from the outside. I like to leave just the faintest "shadow" of the windows visible once everything's sanded down, so I know where to apply the window decals.
Other options to filling them are to apply packing tape to the outside of the fuselage and then fill from the inside with gap-filling superglue. Apply accelerator and then peel off the tape. Another technique is a snake of epoxy putty pushed through the window holes (again from the inside), and smoothed off level with the outside of the fuselage. I've never done this one, but it sounds good given how easy it is to sculpt epoxy putty with a little water before it sets up.
Anyway, do the windws the way you like (and only half the airliner modellers will say you're wrong)
