I am really late to the party, but I get confused if I have separate notebooks or sections. I number notebook pages and write things in order as I am thinking or reading, etc. I make a topical index starting from the back of the notebook by writing the topics as they occur and leaving at least half a page under each for page numbers; some things go under more than one topic. If I try to list topics first, invariably they won’t work out. Since I am working from the back I am free to restructure the index if I need to do that.