In combat, your Flagship or a superior one of another friendly participating fleet will coordinate the attacks of all vessels. The quality of your tactics depends on its capabilities.

Small and basic civilian vessels have no means of guiding your forces. Your pilots will chose the next best target they consider appropriate.

Corvettes, Troop Transports, and Crimson Hives have sufficient skills and resources to guide your pilots, however, their overview of the battlespace is limited. As such, they will direct your vessels to a worthwhile target, but not necessarily the most opportune. Very small and fast vessels may even fly under their radar.

Destroyers and Crimson Cruisers are able to command your fleet, if not perfectly, still very efficiently.

Carriers, Battleships, Command Frigates, Space Stations and Crimson Colossus' are able to perfectly pinpoint the most effective use of each of your forces. They will direct your pilots to the softest target and easiest prize without fail.

Fleets under "avoid combat" orders will not mount a coherent counter-attack, but rather take potshots while trying to flee the theater.