How do you board a local train on a day your using one of your global pass days.

I understand that you must add a local train on a day that your using one of your global pass days but how does it get taken off your ticket? Is there a scanner at most stations that you use? Example I’m using my first day of my global pass to go from Berlin to Munich. First I want to use a local S line to get to Berlin HBF. I’ve added travel from Potsdamer Platz to Berlin HBF. It now shows on my first day ticket. It no longer shows the trip from Berlin to Munich.

Thanks