You have some good ideas already as to how to organize, sort and divide things out. I do much the same. The challenge is to find just the right size, so things fit without wasted space ... or a cubby that is just a tad small.
I keep a "stash" of such ... and when I need something, I can root thru it and solve my dilemma quickly. Another that I like are tin boxes and cans. For all these types of things, what I look for are straight and thin yet solid sides ... less waste space if they can be placed snug together.
Each of my drawers at my sewing machine have similar items, and those that will be used at the same time. Example, all cutting things are together (assorted scissors, trimmers, clippers, rotary blades, stitch rippers, etc.)
Consider what is important to keep out and handy, and have a system for those items too. However, keep in mind the more that is stored away, the tidier your work area will be, and the more inspiring. You can always get out what you need as you need it. I keep a tray by my machine to hold those things. Sometimes they are just too small and either get misplaced, slide under something, or just plain roll away!
The biggest solution to your dilemma ... whatever system you go for, put things back in their place and you'll soon get in the habit of knowing where they are.
................ not that I have that perfected yet, but I am getting better at it!
