How do you all do "deep readings"?

I'm reading a book right now that I am finding fascinating, but I don't want to forget the thoughts and ideas presented in each chapter by the end. I was wondering what you all do when reading books like this. In college, I would usually jot down a few notes on the chapter I was reading, but I always found the act of interrupting my reading to write to be very disruptive.

• Do you take notes and highlight directly in the book, or use another notebook or software?
• Do you take notes as you go, or wait until the end of a chapter or section?

I want to arrive at a system that works well for me, so I'm looking for suggestions here.