Notes extend our memories and enhance our focus. But before building a note-taking system, or taking notes, one should be clear of the purpose of notes.
Decide whether to optimise for review or retrieval practice.
For docs you don’t plan to study extensively, the review is the obvious choice.
For texts you need to master perfectly, the Question Book Method (for theory) or flashcards (for details) saves time.When you want to take notes to read them for pleasure afterwards, highlighting and marginalia could be more suited. But if rediscovery is your desire, a structured system, such as an index of the critical ideas, maybe better.