Star Trek has a bad habit of putting windows on the exterior that really don't align well to interior spaces or that are practical for use for by the crew. The windows on the bottom of the saucers are very impractical for use as windows. However they would be very useful for other things such as science equipment and sensors. So I have no intention of worrying about aligning decks to those windows as I don't think that is terribly important. I'll align the ones that make sense, but the rest I'm dumping into equipment ports and making the decks fit the design. The windows that make sense for crew use I am using to align the decks.