@teatimetrains If you activate the option Activate all timetable shifts in TSW, you can then activate or deactivate the shifts for each route you want to drive in the timetable menu. If you do not activate the option Activate all timetable shifts, you cannot activate or deactivate shifts in the timetables.
In plain terms, it affects the amount of traffic you will see in Timetable. Each layer represents a different type of service you may see on these tracks in real life. However, It's important to remember that this setting does not affected playable services. You can learn more about layers here: https://support.dovetailgames.com/hc/en-us/articles/29235950071314-Timetable-Mode