On and under the deck
Get on the deck on the left and use the switch activated by the sword.  As soldier shoot at the target on the mast. 
In pair grab the chains.  Jump down and go to the lower deck. Take the torch from the column in the middle. 
Scare the tentacles on the right and use the ladder to get down.  Go left and turn the golden helm to move the platform. 
Push the mechanism on the floor in the check pattern.  To move aside the hammock use the wooden wheel. 
When you take the object to the left, again use the golden helm to remove the platforms.  Push the mechanism to the end and on the left. 
Go to the very left with the torch and scare the tentacles on the column. As soldier grab the sword from it  and activate in pair the mechanisms which required that weapon. 
Go lower and take the torch from the middle column in the center of the room.  Set fire to the dynamite in front of the cell on the left.  Enter it.
Switch to the Tattoo Pirate and go up - on the left you will find an orange bar which he can pull.  This will reveal the cannons. You need to set fire to them using the torch (it is on the right on the column). 
On the way to the other ship
Go outside through the cannon hatches. Go right and use Elisabeth's double jump.  Go right jumping on the bars and opening the cannon hatches.
Eventually you will get to the bigger platform. Perform the double jump to get to the other window. A platform with a helm will open. Use the helm.  As Tai get to the abandoned lifeboat. You need his pistol to shoot at the target and lower the chain. 
Jump forward to the wooden balcony. Scare the tentacles with the torch.  At the end of the ship slide down on the rope. 
You will find another ship.  As the Tattoo Pirate rip off the hooks - pull the orange bars.