I see no problem. The station automatically snap to the road. Of course there will be times when there is no proper road to build a station in the town. In this case you make a road and then the station. Also you can use keyboard keys to rotate the station manually.
You can even delete a station to upgrade to a bigger one without losing any of your lines connections. An icon with a time will appear.
My problem is only with hills, bridges and tunnels that are hard to make double tracks. But that is in the todo list to be improved before launch.