I wash mine and the unwashed never gets close to the others until it's washed. I buy the really large plastic storage totes and fold an place in them by either color range, theme, flannel, floral, etc... then I know which one to pull out when I want a certain palette of colors. I have about 15 of those babies stored under my sewing and cutting tables.
I have two 6 foot table I bought from Costco that I use.
Very seldom do I purchase FQ's. Seems like everytime I want to make something a FQ isn't enough fabric.