Here it is though!
Say you have a model in front of you. Scale doesn't matter. It has windows molded in as shallow Depressions. I exclude planes here because Many Airliners, I remember are done this way! We are talking about Ships!' What to do.
A number 2 Pencil, Sharp and fresh. A bottle of "Window Maker" or Good Clear Glosscoat. A small pointed brush. Now, take the pencil, Fill in the wondows and ports(If it has them) With the graphite from the pencil, filling the space completely. Blow away the Graphite dust and then Cover in clear.
Yup! Nice looking Windows and Ports and it's easy peasy. No Matter what colors you used on the Ship. The light catches it just right!