Software, and then recommend popularity. I have used good reader, upad, noteshelf, and the last experience is better. It can be written in many colors and highlighted. A separate page with notes and key marks (I think this is the best and easy to review. But it seems that you can't import directly from itunes. I put it in good reader first, and then I opened it in a remarkable way. Use the lowest stylus. After all, when taking notes, you don't write too much text, and it's not delicate work. Make do with it.