Every student underlines differently and marks different things. So I made a scale: small, underline or circle with the pen; bigger, for whole sentences or lines, the question marker; largest, a dashed box that turns a whole block into one question. You use one tool all the time, or switch as you go.
Pen underlines ran into technical problems in the prototype. They were solved in the real app, where the recognisers were tested on strokes recorded from my iPad: 22 of 22, 9 of 9 and 7 of 7 marks found on three pages. One writer, a few pages: a good sign, not statistics.