I too kept all my spares bits in an old kit box and it eventually sprouted to several. I spent the better part of two days with a minimum of 9 hrs each day spent sorting into parts bins I found at the hardware store that were too low in price to walk away from. Everything is now sorted by Scale, Type (Figure,Armour, Air, Sea) and further broken down from there to Left or Right side (Arm,Leg, Tire etc.) and even further to Country, Time Period etc.
The best piece of advice I can give you is "Don't ask your wife how to organize an area if you want simple results" You will "result" in something that NASA would be proud of, but has taken 18 hours of building time in the process.
Cheers;
Gregory