When Importing, there's the option to include condition, but if you do it sets the box and manual to that condition as well. Is the an option for "Game only" Importing that I have missed.

Also once the games are in there doesn't seem to be options to remove boxes and manuals or set condition l n bulk.

This seems like a fairly straightforward feature, but as a reboxer who cares about the physical condition of his cartridges, but doesn't own a ton of boxes for them, It's a bit of a chore to manually remove the boxes and manuals for the games that don't have them.