try using dvd slim cases for Manuals. I clip the disc retention parts and sand them down and it keeps everything really nice. as a bonus you can edit covers here and put a Manual banner across the top of the spine. This way you can group your manuals together or next to the game.
As a side note. Bagging your manuals is ok, but comic boards are not ok. They will leach the acids from the ink and cause paper to fade and become brittle.