This video shows the AI of the ships. The turrets tracking their targets and attack dives of the smaller fighters. This combat demonstration ran its course without any input from the player. The ships find their targets within range and attack.
The ships are controlling themselves with its own simple AI. Each ship has a preferred target type. Frigates and larger ship types will first target ships of equal size,then target larger ones. Some Turrets on the ships also have a preferred target type. For example ,Point defence turrets focus their fire on missiles and fighters.
You can of course give your ships direct commands to attack a specified target if you so choose.