Nice kit, isn't it? My usual method of filling in the windows is to put a thick strip of plastic card inside the fuselage halve, then fill in the holes with putty. I'd use epoxy putty such as Milliput, if you can, because it does not attack the plastic and any excedent can easily be removed with a rag, toothpicks (in the recessed lines) and some water, the smoothed over with more water. Normally, with this technique, there's no sanding required at all.