Ugh, I know how that goes in a metal shop.
I've take the approach of hierarchical organization. For example, at first, I had all my end mills in a small plastic ice cream pail. Which worked fine, until I acquired a bunch of end mills in bulk lots from a few sources. When it became a pain, it's time to subdivide. Now, end mills are sorted by size. Someday, if THAT becomes a pain, they may get subdivided again into two flute, four flute, HSS or carbide.
For another example, this happened with my plumbing box. When I first started out doing the homeowner thing, all my plumbing crap went in a box. Which is fine when you have just a few odds and ends, and a couple tools. Eventually, that became a disaster. And so, I subdivided. All the copper fittings go *there*, black iron, somewhere else, tools in a separate plumbing tool box. Brass fittings, somewhere else.
As to the mechanics of organizational bins and what not, I don't have that all sorted out. Many organizational products are expensive for what they are.
Maintaining order is a matter of discipline. The last part of the evening is to clean and put away tools, put away stock, put parts for a project in a bin for that project, clean the machines, and sweep the floor. Sometimes it doesn't all happen, but that's the goal.