During naval missions, you will be often attacked by enemy Templar or British units. In order to effectively fight them, you have to learn how to use the weapons of Aquila.
Holding down and then releasing the free run button will launch a powerful cannon volley from the side of the ship, aimed at where the camera is pointing. The path will be marked by a white beam visible on the water. This attack is very powerful, but in order to use it effectively you have to seat the ship's side perfectly towards the enemy.
The second cannon type (swivel gun) is used with the aim button. Hold it down to aim at a target and let go of the button when the changes to red to hit the target. This weapon type can be used to destroy smaller ships, mines and specific elements of an enemy's ship, e.g. gunpowder barrels.
During battles, always attack smaller ships with the swivel gun and swim sideways to bigger units so that you can attack them with a full cannon volley. Also remember no to go full sails as Aquila won't be manoeuvrable enough to avoid enemy fire.
Things are a bit different with attacking forts. When you sail nearby, mortar stands which you need to destroy with a cannon volley will be marked red. For that, swim closer to the shore, turn sideways to the enemy and hold down the free run button to aim at the enemy artillery.
Attacking however isn't the most important part here, as avoiding mortar fire which can damage Aquila considerably is crucial. Each time you hear a warning bell of your ship, go half sails and quickly turn around. Only that way will you be able to avoid the powerful missiles falling in a straight line. Afterwards launch one quick attack and get ready to turn around yet again.