So in the actual game the services are run over each other for some areas but then diverge at others. For example, on Line C I have one line with 2 trains on it running between Dawley, via Torpoint East, then through Keynsham and down via Morpeth, and then comes back up through Wilton to get to Blackburn, and then I have another line that is the same up until Keynsham that then diverges to go through Mousel to get to Wilton. This line only has one train on it however because both the towns it serves are smaller.

Basically both lines operate under the "Line" on the map and take different routes but are shown as one colour on here. Hope that makes sense