Yea, Draenin tried to have an event with this earlier today. As he mentioned - if you turn the boat your player stays in the position he was in... but well - the boat turns. You have to press "A" to deactive it and then quickly run back to the pilots position.
Also, if you hope off the pilot position, and you're too close to the cannons... you can't use them. You have to run away from them and then back, this is very critical when you're trying to shoot another boat.
Otherwise they seem to function as they should, besides being throw off if you try to go below deck... and sometimes not being able to get on
...