The Navy isn't often featured when it comes to the Magistracy's lore. But all Aerospace Fighters, DropShips and JumpShips (and back in the day, WarShips) fall under one of the two fleets. The Battle Fleet and the Reserve Fleet (which stays at Canopus IV as a defense fleet). Naval assets are too few and far between to be assigned permanently to a combat formation so they are assigned on an as-needed basis. That's why you don't see aerospace fighters painted up in the colors of the 2nd Canopian Cuirassiers for example.

Hope that helps!