I print out inlays on the occasion for my NES, SNES & N64 covers. Usually when i replace an old cover with a better one, a correction or in a "collection style" i just flip it inside out so i can see the old cover on the inside.
Most recently I have been printing out my alternate versions of the vertical n64 covers (ie one with a green spine and one with a different color spine and back ...zelda comes to mind) on the backside of the normal cover. That way it looks nice and uniform all line up but i have the other version of the cover on the inside.