one thing I've noticed is that a lot of times when people read and take notes (or even listen to lecture and take notes) they try to transcribe almost everything and the focus winds up being on writing the notes vs. taking in/understanding the material. Your reading (or listening) tends to be more broken and interupted while taking notes which can impede putting together the picture for understanding.
So less is more for starters. In reading a book, I would just read through once for understanding w/o taking notes the first time. Once you've read through it the first time and understand things. Then go back and take notes only on the highlights/important stuff. Even though you're making two passes, you'll probably find that it goes faster than one pass of read/stop/take notes.
When taking notes, you can use pictures, mnemonics, etc. But ultimately, the more you understand, the less you need to worry about memorizing (though in some cases memorization is pretty unavoidable)