They're excellent in a stack with starships, especially since flagships and zenith starships have the same 18 speed. If human colony rebellions are on, you can stack them with rebel fighter/bombers and frigates for a single group that can pretty much wipe out entire planets by itself.
I would recommend sending them out to attack, since they have high range, good speed, lots of HP, and a bonus against turrets. They don't really have the speed or firepower to be that great on defense - you can't shuttle them around fast enough to meet raids, and they don't zap quickly enough to stop a raid dead before it gets your command station.