Here is hints and tips on how to organize your shop. The actual process and some of the organizational accessories.
Step 1: Sorting
Decide what each box, bin, or Ziploc bag is going to be for.(or decide as you go.) start throwing all the misc. tools in a box. All the scrap metal in another, Cords and electronics in another, Welding supply, specialty tools, nuts & bolts & screws & nails, Epoxies, whatever you work with just organize it in some manner.