How do you keep track of ideas when reading nonfiction?

When I read information- or idea-heavy books, everything starts to feel jumbled in my head. Sometimes it also feels like the author is repeating the same points in different ways.

I've tried making an outline from the chapter headings, but it didn't really stick.

How do you read nonfiction so that, when you finish the book, you’re left with a clear, meaningful picture of how all the ideas fit together?