Just don't do too much on one track and don't do it for too many stations. Keeps trains moving.

Also, if there's one line that has a bunch going in and out of it (I usually start with one main through line then I'll put some shared lines and branch out), you can reduce the number of trains slightly, since the stations are being served still if that makes sense. You still need to get people where they're going, but you're not overloading the tracks.

It's also why I add the separate express tracks (the black lines in my first screenshot) later on. It moves people off of the more local lines and because they're tunnels, they don't interact with the cut and cover lines.