So I've tried to make a func_tracktrain in the 3D Skybox sync to a func_tracktrain in the regular map. I've tried setting the skybox's tracktrain to the track in the map, but it doesn't work. I also tried copying them and putting that in the skybox, but that doesn't work either. It moves right, but the skybox brush itself is not aligned with the map brush. What am I doing wrong?
The way Valve did it was that the had two separate trains, one for the skybox, and the other for the game. They get the trains to change behind the train shed, I believe.
What lilatomic said. they used the shed to activate the one on the skybox or the one in the map. If you listen to the developer commentary on cp_well they explain it pretty throughly.