For students, coloring texts with markers has become something of a sport. The result is sheets of paper that glow yellow or orange or green, with words and sentences that are even harder to read than before. This habit is just as terrible as the one of wanting to take down every single word a lecturer says in bullet point form. In the excitement of writing down every thought, the student forgets to understand the thoughts and, perhaps more importantly, the personality of the lecturer, the context of the thoughts.
To be sure, it can be useful to excerpt books and essays. But in the first place, let the content enrich you. You don’t have to highlight entire sentences. It’s often enough to bracket individual words or phrases in pencil so you can quickly find them later when you’re flipping through the pages. Or make notes in the margins according to a scheme you decide on yourself. You might use exclamation points for important thoughts, question marks for unclear passages, etc. Write keywords in the margin. But please don’t highlight half the text just so you feel like you’ve read it.
You should not only read it, you should understand it. Especially for more extensive theses, it can of course be useful to create an index card system with citations and references, small summaries. But for the important literature, the sources, this should be less necessary because you know it so well that the most important thing is in your head.