The second Map scrap is one of three items found during Ghosts Ahoy needed to create the treasure map. All three scraps must be in the inventory, and then any scrap can be used on another to form the complete treasure map.
The second map scrap is found near the Ghost ship wreckage. From the main level, cross the gang plank to the north and jump from rock to rock in the following order: North, West, West, North, North, West. Open the chest on this last rock, then jump back the way you came to get back to the pirate ship.