Every second wasted searching for tools on your desk is a penny or two from your income.
On the other hand, super organization and making nooks and special boxes and cranies for each and every tools only work for those whose mind is hard wired that way to begin with. Trying to do this is even more of a waste of precious time.
What I use is the "logical heap method" I have a several trays from the 100 yen store that I put certain types of tools into when I use them. I've trained myself to always put certain tools in certain trays, but nothing beyond that. So there's always a heap of tools in the tray in no discernible order. But, at least, my hand will always go to the right tray and in just a few moments of fumbling around, I'll come up with what I need.
This has saved me endless amounts of time and "lost" tools.
Another thing I do is when I'm done for the day I dump each tool into their respective tray, so I'll know where they are when I go to work tomorrow.
But I also believe that the God of Small Things demands the occasional sacrifice and has many Gremlins at her command. Things disappear in my shop too, only to mysteriously reappear six months later.
But at least my logical heap method keeps this well down from what it used to be