Farnam Street with tips on how to read better and take notes, I particularly liked this view on marginalia:
Think of reading as a conversation between you and the author. One of the ways you can process a conversation with someone who is not there is to write in the margins. It’s ok to question the author or disagree. This is how we think.
Farnam Street cites author Mortimer J. Adler from “How to Read a Book”:
Reading a book should be a conversation between you and the author. Presumably, he knows more about the subject than you do; if not, you probably should not be bothering with his book. But understanding is a two-way operation; the learner has to question himself and question the teacher. He even has to be willing to argue with the teacher, once he understands what the teacher is saying. Marking a book is literally an expression of your differences or your agreements with the author. It is the highest respect you can pay him.
They follow with some tips for note-taking:
At the end of each chapter write a few bullet points that summarize what you’ve read and make it personal if you can — that is, apply it to something in your life. Also, note any unanswered questions. When you’re done the book, put it down for a week.
Pick up the book again and go through all your notes. Most of these will be garbage but there will be lots you want to remember. Write the good stuff on the inside cover of the book along with a page number.
Copy out the excerpts by hand or take a picture of them to pop into [archive]. Tag accordingly.