A trip on the train would go like this:
1.Get to the station and board the waiting roof-car.
2.The train passes the station and your roof-car is picked up.
3.You get off the roof-car and sit down on the main train below.
4.Approaching your stop, you board the roof-car.
5.As the main train passes the station the car stops and you get off.
Simple and brilliant, just gotta make sure all the kinks are worked out first.