I did the same for all the hardware in all the kits for the RV-10. I got several of those multi-drawer storage things from HD or Lowes and labeled the drawers A1, A2, A,3, B1, B2, B3 - then as I put stuff in the drawers while inventorying the kit I would note the location in the spreadsheet.
THen I could sort the file by location, part number, description, etc. as needed.
Once done I could consolidate like part numbers in one bin saving space.
Since the drawers were generically labeled I could recycle space as parts were used up, etc.
After I was done I did move common parts near each other - like all the nuts together, etc. But not perfectly.
I keep a hardcopy of the spreadsheet sorted by part number and when I need an AN-XYX-42 or whatever I know exactly where to look for it. I also got some small bins that look like larger tubs but maybe 6"x4"x4" that I put put larger small airplane parts in. Using the labeling scheme you can use whatever location you want as long as you label it. One drawer of my rollaway toolbox has a number of bins in it for common hardware with weach bin labeled.
I got tired of trying to chase stupid parts down. Took awhile to set up but not all that much more than just inventorying the parts in the first place.