I store embellishments by categories and color. When you make the change its a daunting task but well worth the effort.
I store all small items like buttons, brads, charms, and beads in divider boxes by colors (red, pink, blue, gold, silver, clear, white, antique, etc.) The other
divider boxes I have are for letters, insects, birds.
I store larger items in categories (hearts, hinges, tiles, garden, sky, etc.) in clear boxes from
Harbor Freight. I put small items in the little boxes and then just lay larger items inside the boxes. These boxes are stored in DVD baskets from Ikea (no longer available).
All stickers/paper items are stored in plastic envelopes similar to
these
Some things are just tossed in a basket because I have a lot of them and they don't need to be sorted. I don't mix multiple kinds of things in a basket but I do store the tools that are used only for that item. Example - the wire basket has wire and winding tools, clay tile basket has the tiles and the etching tools. In the baskets are flower soft, etc.
Paper flowers are stored by color in clear canisters from the $store.
A key item is that once you sort everything out, think about what is the easiest way to put everything back in it's area. Some storage items are pretty but they really aren't functional. By putting boring storage boxes inside baskets, I get functional and pretty KWIM?
Also, buy a couple of extra boxes because I found that when I needed more of an item, it had been discontinued (like the Ikea DVD boxes)
With this system I can find what I want by color and category. I don't do things really in "themes". I don't keep original packaging as when I use something up I don't replace it. I make myself find something else that I already have. Also, having things in boxes and baskets, protects them from the sun & dust and they are hidden but within easy reach. Oh - all my baskets are labeled because they all look alike so I'd never remember what was inside ;)
One warning - if I'm looking for a particular charm and I can't remember if it's gold or silver, I have to look in multiple boxes to find it - but I always find it.