Yeah, agree with KokiriChild. I think it's good collecting sense to not pay much for a beat up box, even on a somewhat rare or popular game. I've actually been to one local game store that discounts their CIB's based on condition. It's pretty rare, but I think good business.
As far as upgrading, though, might I suggest that, unless space is a serious concern, you keep the beat up boxes along with any upgrades? Then your collection tells a story of how it has grown over time. If anyone asks why you have 3 copies of, say, Super Mario Bros. in the box, you can relate how and why you got them.