I'm not anywhere near that organized, but I do have a pretty simple method for keeping track of my tools. They are somewhat laid out in each drawer by size. When I put them back in the box and lay them in order....
When I was working on other peoples stuff, I was very good at making sure everything was back in the box where it belonged. I didn't loose many tools that way. Now that I'm retired and working on my own junk, I'm not so fanatic about putting the tools away at the end of the day, it more like once a week these days. I do have a place on my bench I pile the tools between the days they get put away. If I'm working on a specific area and I didn't get done at the end of the day, I will leave the tools at that location for the next time.