For windows, you have a couple of choices...
You can open them up, Like Steve did here, paint the entire model and fill them in with Testors (or any other brand) window maker. You just touch the tip to one corner of the opening and pull it around. Surface tension keeps it solid across the gap and it solidifies into a nice semi-clear window that dissipates the light across the opening. This process works for smaller-scale windows like this.
If the ship is larger, it would need clear acrylic or styrene inserts. (or actual clear sheet). You can also leave open holes.
The problem with just leaving the windows "OPEN" is, if they are large-enough, you can see inside the model and you get "hot spots" where you can see the lights inside as you move it around... Unless you install a physical interior.
I plan to make it just like the DS-9 model in Sisko's office, so Greg's original didn't have lighting; just black rectangles (thank God).
Also, you should take into account "scale lighting". People put BLINDING lights inside their models and it blasts out of the tiny windows and everyone says: "Great job!" "It looks cooool!"
No, it doesn't. If this was a real ship, the crew would be BLIND with the interior being so bright. Take a look at high-rise buildings, in large cities, from a distance. You can use that as a guideline as to how bright model ship windows should be.
If they are too bright, or not located properly, it gives the model a goofy, toy-like quality. I have been building models professionally since around 1990, so I have seen a lot of badly lit models. (some of them were mine :lol )
So you can do a stellar paintjob and weathering, but if the lighting isn't right, it really kills the model over-all.
Let's be careful out there...
(hops off of soapbox).
Hijack over. :lol