I can't claim to do everything, or even most things right but I have been happy with how I keep track of the parts/hardware. I use the inventory list that comes with the kits (fuselage, wings, finishing...) and on it you can see all the bags and what is included in each bag. I keep the bags numerically on a shelf and try to cross off the parts on the inventory as I use them up. Sure I dump bulk rivets, screws, bolts and nuts out but for all the odd/special hardware it makes it easy to find when I need it.
Keep building,
KC