I always used to keep my carts loose and my boxes and manuals in a seperate box. That way you still have both and don't have to worry about messing up the boxes. It worked fine for me untill the box they were in magically dissapeared when my parents moved while I was away at college

Also, I don't like how some game stores when you take the box for a game up to the counter they sometimes just give you the cart...only occasionally do you get a box or manual...and rarely both. Does this happen other places?