You need to compartmentalise, each nut/bolt/washer etc should have it's own specific compartment/location, preferably with a soft bed of tissue or foam to cosset said part and prevent any scratching or chafing.
Of course all parts should be organised by colour and/or use.
ps: now I know why I have such a hard time finding particular anno bolts, you're hoarding the worlds supply of anno bits in that bloody box!!