Well, the first thing you should realize is theres a small little bug. Avoidable (i think
) but definatly fixable.
Seems to happen when you manually man the guns yourself. What will happen after that is the AI gunner just sits there like a dummy. Quickly manning the gun, pointing it in the direction of the oncoming aircraft, and firing.... usually does the trick. After "showing the crewman how", the AI seems to get a clue.
Other then that, make sure you have the correct settings on the flak guns via the watch officer. Personnaly i tend to have them, set to "engage closing targets" and "engage any aircraft". That way they fire at whatevers doing an attack run, and not wasting ammo on things they can't hit, or things that are not an immediate threat.