Welcome to the Quilting Board!
I had one of those boxes used to store embroidery thread on bobbins that I wasn't using. I started using it for some of the small items you mentioned. It is see through, so it's easy to see what's in there. It has been a workable solution for me. It fits in my cabinets and they are stackable.
I think being organized 'once and for all' would only work if one never ever bought any new items to join the party.
So - when organizing/stashing/filing - I think it's good to leave a little wiggle room for possible new additions.
Another way of stowing things might be by 'frequency of use' - the items one uses often would be kept really handy - and the ones that one vaguely remembers having and were last used ten years ago - could be stashed in clear boxes 'up high' on the shelves.
I don't have a particularly 'good' system, either - and I'm gradually learning that 'more' is not always 'better'
I use a large pegboard mounted on the wall by my machine. Scissors, rotary blades, seam rippers are either hung directly on long hooks or put in zipper baggies with a hole cut in the top below the zipper to fit on a hook. Everything's in plain view and easy to find.
I give up really! One project and everything is a mess but these storage ideas my motivate me to take another look.
Experience is simply the name we give our mistakes.
I like the shoe bag thingy. Same fabric I used to make my daughter a Big Board and sewing machine cover. As far as my storing, I use those plastic drawer thingy from Walmart..I have 4 stacked 2 high and side by side for some of the bigger stuff. I also store other non sewing things in them. I use the plastic shoe boxes to store most of the little stuff like ribbon, trims, zippers, crafty stuff. I TRY to keep things pretty organized, but we all know what happens when we start something new and start looking through the stash !! I also made wood shelves in the closet to stack the plastic storage containers with fabric. I had them stacked 4 high on top of one another and the bottom containers got all smashed up from the weight. Look luck, it's a tough job !!
plastic bins, plastic shoe boxes, and a Big peg board for me.
I have gotten organized "for once and for all" about a million times! Funny thing is that we keep coming up with new toys that defy description. I reorganize my sewing room about once a month because every new project creates a new mess...
I do try to sort stuff in 2 different ways. One is by place of use. Next to each sewing machine (2) I have scissors, pin holder, bobbin thread ring, 6 inch ruler, box for presser feet and accessories. Have the same for the long arm. By the ironing board I have iron cleaner, starch, press cloths, teflon applique sheet, scissors for trimming odd raveling threads. The second way I sort is by type of tool. All rulers are hung on the back of a door from a metal shoe rack with plastic spring clips. All templates and odd shape things like pressing bars, tube turners, flexible rulers, circle cutters, compass for making circles are in an open plastic bin. All fabric markers are in a container, permanent markers and pencils are in another container. Scissors and hoops are on the pegboard. Piecing thread is in a drawer near the sewing machines, quilting thread is on a rack by the long arm. This works for me (most of the time)!