I tried breaking up kits, and it about gave me a heart attack.
I'm a kit scrapper, so I rarely go outside of a kit to search for something. So since that's how I scrap, I organize by store, then designer. Within the designer folder, I have a folder for kits, and a folder for everything else (element packs, freebies). Within the kit folder are folders for AP, EP, and PP.
I love my alpha's but I tend to forget about the awesome alphas that come in kits. So I recently started breaking out all my SSD alpha's into one main alpha folder. They get labeled with the designer and kit name so that I can quickly see if there's an alpha that matches the kit I'm using (if I've broken the alpha out).