I'm always in a constant state of reorganization as new stuff comes in, stuff gets used/installed, and other stuff goes out.
Labels also go a long way to making things easy to find.
I also try to subscribe to the practice of "First Order Retrievability". That is, organizing things in such away so that you should never have to move one tool/item/box to get to something else. Hard to practice 100% of the time, but it sure helps with organization and being able to scan and do a quick inventory of parts and what you might need.