I recently started writing in my books when I read them. It has made the single biggest difference in remembering and understanding what I've read. I don't think I can ever go back again.
Unfortunately, there isn't any good ebook substitute for writing in an actual book, or at least I haven't found it. The best I've found is Adobe Reader, which says something about how little most ebook platforms know about writing in books. But even with a proper writing capability, no software will be able to smoothly flip back to another part of the book when I want to refer to what the author said earlier.
Ebooks hold the same place in my mind as LibreOffice: both are a good cheap substitute for the real thing, but only if you don't intend on using them in any sort of serious capacity. I read the Hunger Games on eBook, and that went fine, but that's only because those books weren't important or life-changing. But if you really want to fully understand a book, you need to buy the copy that's made out of dead trees, and fill the important parts with so much ink that you can barely read the original words.