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Destroying them will usually give you the Guardian and War Hero awards, giving you extra protection/damage. If you don't have the War Hero award yet, then try to kill a few fighters on the way. The recommended order to take them out is: Shields, of course. Just fly along the ship's length, so that all of your bombs are sure to hit. Unload all six at the same time. Engines Bridge Communications Sensors Life Support

Summary:
Hop in a bomber and go to the enemy frigates. Go to the enemy capital ship. Bomb the critical systems.