1. "Never read a book without a pen in your hand." ~ Benjamin Franklin - That's great advice whether you write in your books or take notes in a notebook. Personally, I write, scribble, highlight, argue and draw symbols in all my books.
2. Read a whole paragraph / section BEFORE you stop to highlight or take a note. Don't stop right when you see something interesting; keep reading to get the "big picture" or context of what stood out to you. Then "reread" when you make your notes.