Based on my observations and trying to get ships to work with my Costa Rica and Nicaragua maps, it is almost impossible to get ships to work properly without a band of water at least 7 cells wide all around the land. Ships appear to enter around the center of
each [a] side of the map and then travel from there. If there is no demand for them, they will sometimes appear and just sit there at the edge of the map for a while.
Each ship is associated with a Port with a yellow arrow just as each of the Port's employees is so identified. That is not a surprise since a ship is a "unit" like each person.
It is also not a surprise that ships appear on the side of the map closest to the Port to which they are attached.