They differ in the number of cannons they carry, the number of moves and actions they have per turn, and the resources they start with.
A ship can perform the following moves and actions:
Looting and capturing require you to place the ship either adjacent or diagonal to the target, but not more than one field away.
If the ship moves forward in the direction of the wind, it gets one additional move.
Each turn, the crew of a ship consumes rum. If the ship is out of rum, the morale of the crew is low. This decreases the ship's effectiveness in combat.
Each turn, the ships that carry gold transfer a small part of their gold to you.
Each ship can fire its cannons on its port side (left) or its starboard side (right). If the cannons hit their target depends on which side of the enemy ship they are targeting, and the accuracy of the shot. Immovable targets like shipwrecks or obstacles are destroyed by one shot.
The chance of hitting the broadside of a ship is higher than the chance of hitting the bow (front) or stern (back). A hit to the broadside will yield regular damage. The bow and stern are more difficult to hit because the target area is smaller. However, if the shot hits it does more damage because the projectile travels through the length of the ship, potentially hitting more targets. Especially the stern is weak to cannon fire because of its flat surface. A hit to the rudder can render the ship not maneuverable.
Destroying a ship increases your crew's experience in combat.
Besides the regular cannon shot you can attempt to hit the masts with a chain shot. If you succeed, the ship cannot move until the mast is repaired.
Your third option is to lay mines. They can be used to defend a fort or to damage ships that are trying to follow you.
If a ship is next to the Commander at the beginning of a turn, the crew gains courage. This increases the ship's effectiveness in combat.
You can build and upgrade ships at your forts. Building and upgrading ships costs gold and takes one turn. Upgrading a ship restocks its resources.
You can capture a fort if it is not already captured. To capture a fort that it is already captured, you first have to destroy its defenses. Capturing a fort takes one turn.
Each turn, a captured fort will repair its defenses.
Each turn, a captured fort generates gold for you.