Ports are reskinned train stops and need to be placed adjacent to a track (water-way). the graphics don't exactly match the selection boxes, you need to play around with it a little to find the right spot. And depending on the direction you're ships will be going, the port either needs to be placed on the land facing side of the waerway or the water-facing side. in the first case use "land based port", in the second the regular "port".
