One person needs to board the skeleton ship and then make their way down to the brig area, located at the front of the lowest deck. The doorway to the brig is a choke point where skeletons will have to pass through if they want to attack you. They can't shoot you through the bars, and by standing on either side of the doorway you can swing your cutlass to damage enemies attempting to enter before they do so.
Now you just need the other person/people to damage the front of their hull at the lowest point, either with cannon fire, by crashing into the ship, or by letting the ship crash into you. A hole will then be made inside of the brig (the choke point) and it will simply be a case of preventing them from fixing this one hole.
Using explosive barrels is not recommended, as you may kill the person defending the hole, as well as yourself. This dosn't work against the plant skeleton variant.
