Yes, I do read everything in print. I tried using an e-reader several years ago, but my comprehension was crap, so I put away the e-reader and turned back to reading physical copies again.

But yes, there are still ways to document the best ideas, notes, and quotes from e-books. Two ideas for you — one digital and one physical:

1. Digital — You should be able to copy and paste info from the e-reader (depending on the e-reader) into an app like Evernote or Day One. Both of those apps are great for storing and tagging ideas.
2. Physical — You can handwrite notes from the book into some type of commonplace book. For example, I write notes on 3x5 notecards and catalog them into topics in a notecard box.

Best of luck and thanks for reading, Marek!