A few hours or even days spent organising your workshop storage systems is very well worth the time taken. Of course, you have to abide by your own housekeeping rules and if this goes against your nature or abilties, then you just have to try to enjoy subsequent time-wasting.
I think it helps to think more clearly about the logics if you
I would never put things e.g. taps of different systems together. I can go for weeks not needing SAE/Whit/BSF taps, so why have to sort through them? All my 'popular' taps and drills; tapping, taper, second, plug and clearance are fitted into marked holes drilled in an overhead wooden beam, so are immedately accessible but out of the way.
Wherever possible it is helpful to have such things as O-rings, washers, nuts and bolts in shallow trays or boxes, stacking if necessary, so that they can be picked over without having to tip them out onto a cleared area of bench.
Home-made wooden dividers in drawers are handy for stopping calipers and mics, depth gauges etc from entangling.
I keep the dozen or so different grades of emery paper in individual A4 envelopes to stop them contaminating each other but I would prefer very shallow drawers.
Heavy items stored on shelves under the bench are useful for holding it down.
Something as important as this needs to be thought about and sketched before even going into the workshop, because once you are there you might be tempted to take the easy wat and cut corners, resulting in illogical arrangement.