Once you have completed the main story mission aboard the Aquila in Sequence 5, you will unlock Naval Missions. There are 4 of these to complete ("The Chase", "The Rescue", "French Involvement" and "Biddle's Hideout") and they must be done in sequence, although they can be replayed later if you fail to get 100% sync. To initiate them you will need to talk to any Harbourmaster, labelled by the anchor symbol on the map.

The basic premise of these missions is to destroy the enemy ships, before they sink you.

Please see below a list of the fundamental controls you need to be aware of when sailing the ship:

Steers the rudder.
Camera.
Increase speed but decrease manoeuvrability by opening sails.
Decrease speed but increase manoeuvrability by taking down sails.
Brace to reduce damage from incoming fire and tidal waves.
Fire deck-mounted swivel guns. Hold down the button until the target goes red, then release.
Fire a broadside cannon volley. Hold down until ships pass along the side of your boat, then fire.
Select primary cannon ammo type.