Towns represent major areas on your layout, and help your train crew know where they're going. If the location isn't on the visible layout, then you can mark a town as "in staging". Towns in staging are special because if a freight car arrives at a yard in that town and is destined for any other non-visible place on the layout (either a town represented by staging or a town that's offline), then the car is treated as if it arrived at its final destination.
In effect, once the freight car goes off the visible layout, then any stop it makes should unload it and send it off on its next journey.