Well I keep spare parts for same chassis types in different boxes:
I mean I have a SS box with all racing buggies spares, a second box for all new tires and a third for used tires.
This happens to blackfoot/mbeetle parts too and other models.
For my 3speed truck I keep them divided into hilux/blazer and bruiser/mounty, a box for used parts and a box for new parts, a box for all tires, a box for all used body parts and a box for misc new parts (plastic trees, wheels, whindshields, radiobox etc)
Screws/nuts/grubs/etc are divided into 4 boxes: 2 screws divided into used/new and 2 nuts/spacers/etc used/new. Special screws are in the box with proper chassis parts.
I'd say start with a generic box and put what you have into it, even if you have 1 piece. In the beginning I had 1 box for 3speed parts with all hilux/blazer/bruiser/mounty used/new parts, now parts grew up and I added other boxes. I use a lot of pc keyboard boxes, find them very usefull and can easily find them at work.
What is harder is to remember the parts I have.
cheers
Roby