There's only one right way for a toolbox layout.
Whatever you feel most comfortable with is the best setup for you.
Example...
I had two drawers one with wrenches and one that wasnt. For some bizarre reason I'd always go for a wrench but I'd open the "next to" but wrong, drawer.
I switched that ****.
That said you don't want wasted space. In other words screwdrivers in a 3 inch deep drawer.
Some things aren't worthy of the tool box and perhaps you can get a cheap shelf or a shelf under a table.
My wheel bearing sockets are in a big case. They're already organized so I shelf those. I've got a nice set of snap ring pliers from SO...in a nice case. They get shelved. Also shelved, mitey vac, SUR&R fuel line kit, slide hammer kit, dremel, battery tester, and a few others I'm forgetting..
But the key is all those shelved have a decent case already and would just kill the space in my box which I'm jammed full as is.
You'll probably rearrage a few times until it just feels right for you.
Good luck.