The printed daf that we use today was set hundreds of years ago. If I add in markings, aren I changing that?
To answer this, one must appreciate how a great talmid chacham learns a daf Gemara: He will map out the entire sugya, highlighting key names and phrases ― all in his “mind’s eye.” Unfortunately most of us are not blessed with such genius, particularly over the course of 2,711 daf. With the markings, we can begin to approach this level of clarity. The Gemara Marking System does not add or subtract one iota from the Gemara text. A pencil is merely used to add “notes” into one’s Gemara, in the form of lines and shapes, as an aid to understanding and remembering. Everyone accepts the idea of writing down Torah sh’Ba’al Peh for this purpose.