Stickers, diecuts, and rub-ons are some of the hardest things to organize because the different sizes and shapes pose many challenges. Rub-ons present their own challenges because if they aren't stored properly, they stick to each other, damaging precious supplies.
SORT: time to be ruthless. Consider if you are really going to use these items. If you bought a whole sheet of die cut just to use one or two tags, why are you hanging on to the whole sheet? Those stickers you bought in 1999 were adorable then, but definitely not your style now, are they? So, sort into piles: TRASH, SELL, DONATE, TO KEEP
PURGE: Throw out the TRASH pile. Bag up, and assign a price and your initials to the SELL pile and put them directly into the garage sale box. Make immediate arrangements to rid yourself of the DONATE items.
ASSIGN: The KEEP items need to be divided into categories that make sense to you: by colour, by manufacturer, theme, size, or type.
CONTAINERIZE: Here is an article about storing stickers, diecuts and rub-ons: http://www.simplyorganized.me/2011/12/scrapbook-organization-stickers.html
EQUALIZE: take a few minutes at the end of each scrap session, and whenever you return from a crop or a shopping trip to put your stickers, rub-ons and diecuts where they belong.