In the 4th edition of Settlers there is a pre-determined map that the instructions provide. It tells you were to place the tiles and numbers, how to connect the sea edge, how to place the tiles in the sea edge, and also starting positions. It is a balanced map and it avoids initial settlement placement which can be hard for beginners. The harbors on the sea edges are for this map. The harbor pieces are for randomizing your harbors if you chose to not use this map.
It doesn't matter where the harbors are at. What matters is if something like a 6 or 8 wood is placed next to the wood harbor.It DOES matter where the 3:1 harbors are located. The game feels much different if they are scattered evenly than when they are all on the same side of the board.