why not both? mark up the book while you're reading, reflect in your notebook on what you read

The notes only make sense with context. I'm not interested in copying three or so sentences for every small comment or even just a highlight.

Do you have tips to start using notebooks instead of marking books? I personally like to underline stuff in my books, when I start a new novel it's often people, places and events. I'm not sure what would be the notebook equivalent of that. Writing down what I would underline? It seems tedious and you loose context and the sense of proximity between words.

Who said anything about throwing the book away?