Whenever I build a new model or rebuild an older one, I always make sure to keep track of the parts. Foam egg containers work nicely for the small parts, screws, bearings, diff balls etc. I also keep a nice selection of smaller pencil/cigar boxes around for suspension arms and other larger parts. Sandwich baggies come in pretty handy too.
Organization
Did you drop that tweezer sized clip in the carpet? Slide a piece of nylon stocking over the end of your shop-vac and tape it in place. Then sweep the area where you think you lost that little bugger and it will be sucked into the nylon. Just remember to grab it or place the nylon over a paper plate before you turn off the suction. Otherwise you’ll be starting over.