I keep anything Metric in a separate top box and mid box. Most all specialty tools like brake tools, timing lights etc all go into another separate box, all standard tools go in my main box, although these days I find I dig more and more tools out of my Metric box instead of my standard box. I keep all of my drives stored separately, IE all 1/4" is in one drawer, all 3/8" sockets in another drawer, too many 3/8" sockets to store 3/8" drive tools in the same drawer as the sockets so the 3?8" drive tools get their own drawer right above the 3/8" sockets. All my 1/2" sockets and drive tools are in the very top of my main box stored together.
You probably do not have the room to do the separate box thing though I suspect. Here is a great suggestion for crow foot sockets. For 3/8" drive crows buy the Snap on two piece crowfoot holders. They are super for saving space in your box and even better they are not costly. I have a set of 1/2" crows as well and to store them in a compact way I took a piece of 1/2" key stock, slid all of my crows on the key stock and once I knew the length I needed I cut the key stock to the length I needed and left just enough extra to cross drill each end of the key stock and shoved a spring keeper that is easily removed by hand in each end. It keeps the crows stored nice and compact. I am always looking for ways to save room in drawers and this was one great solution.
OOPS, I JUST NOTICED THAT YOU ALREADY HAVE THE 3/8" CROW HOLDERS! COOL!