For my Atari 2600 games, since the manuals are slightly too large to fit inside the case, what I've been doing is actually slip it inside the sleeve under the cover, with the manual cover pointing inside, that way when you open it, there's actually graphics of the original manual, and it keeps them safe. Others, such as SNES or Genesis, I just stick the manual inside the case loose, I just open it flat so that they don't fall out.