How to order a group of ships to protect a specific area?
Simply order your ships to move to the intended coordinates and leave them on the default Defensive Stance known as 'Neutral'. They will attack nearby enemies and try to dodge enemy weapons fire. Note; they will chase enemies if you put them on 'Aggressive' and not fire back on 'Evasive'.
The unit AI is of course fairly limited as is standard for an RTS. You may have better results micromanaging units especially against a human player.