After completing one of the main story missions, you will become the owner and captain of the Assassin flagship, Aquila. Using it you will be able to head onto special naval missions, earning money and unlocking sea trade routes. In order to view available missions, head to the harbor nearby Achilles' house and speak with the overseer. A description of all the missions will be added to the guide later on.
The rudder is controlled with the left analog stick, while speed is mapped under two buttons, respectively the jump and interaction button. Pressing the first button once will cause the ship to go to half sails, giving you less speed but increasing manoeuvrability. Pressing the button again will set the sails completely and let you reach maximum speed.
Out in the sea, always try to go with the wind, the direction of which can be seen on the mini-map in the lower left corner of the map. Green arrow means that you're sailing with the wind and red against the wind.
During storms, you will additionally have to look out for waves hitting the deck. When you that one is about to hit the ship, press the attack button to make Connor hide and avoid being knocked over.