Petri Bloomqvist, in a picture for one of the "Ships of the Line" calendars, depicted the rectangle under the fantail as a hatch for two or three workbees (a notion I rather like and subsequently pinched
). As for the rest, they make a lot of sense, to me at least, as access hatches to the antimatter generators and storage pods, with the circular yellow one indicating the intermix chamber, specifically, the ejection port. The remastered version of "Operation: Annihilate!" shows it opening up like bomb bay doors, to allow orbital insertion of those ultraviolet satellites, so I've modified the internal setup slightly to allow for a couple of crewman in environmental suits booting those things out the hatch, not unlike how crewmen on AC-130's pitch flares out the side hatch during night operations.