Loose papers are the bane of many PhotoReaders.
I don't know if any one way works better than another. Play with it and see what works best for you.
When I've punched things for a note book, I find the pages getting caught on the rings when trying to flip the pages.
PhotoReading off a computer is great. I just did a television show where I demonstrated it.
With that said, the time you spend, however, scanning material for the computer is probably better spent doing virtually anything else. Geez, come over and mow my lawn! I'd just PhotoRead it regularly.