I store my stash in a couple different ways. If I have a series of fabrics that will make a quilt, those go together and I have a notebook with the patterns and colored pictures of the fabrics so I won't forget what kind of quilt I am making with that fabric. Then the "Just have to have this fabric because" I store that by color. I have mine stored on plastic boards that are acid free, but hold the fabric much like it does at the store, except I fold it in half one more time.
You will find that something may work right now, but maybe at a later date, you aren't happy with the way it is stored and you can start again and use a different system. In other words, your storage system will evolve as time goes on. Good luck and be sure to post pictures when you are finished.