My system is an extension of what I had when I had my own Porsche shop.
There I had really big tool box, a smaller cart with 2 drawers and 2 shelves, and a bench with many plastic boxes of specialty tools. The small cart had all the stuff that I used on every job.
Now I have a medium tool bag with all of my fractional 1/4" & 3/8" ratchets and extensions, fractional wrenches under 3/4", my favorite pliers (several), about half of my screwdrivers, 2 hammers, a small pry bar, most of my small stuff, all the stuff I use on almost every job. Next is a large bag with the rest of my screwdrivers, all my 1/2" fractional stuff, bigger hammers and pry bars, scrapers and big wrenches, most of the rest of my stuff.
I have a bag of drill bits that I keep with the drill, a bag of taps and dies, hole saws in a plastic case and other weird stuff like a piston ring compressor, a valve spring comressor and other things I hope I never need stored mostly in a single area but not in a bag right next to my spare parts that I also hope I never need. Lastly (almost) I have all my metric stuff that I use only on my outboard in a smaller bag in that same area. Beyond all that I have a small junk drawer that has a slot and a phillips screwdriver, a small pair of Knipex pliers, and a small crescent wrench.
The very last part is stuff like my big 3' prybar and other long things that won't fit anywhere that the rest of the tools belong that I store down next to the engine.
Tool bags really suck compared to my huge Snap-on box but I wouldn't go back to fixing cars every day.