Whether you store on comic boards; fabric bolts; etc. as suggested previously, I would suggest sorting by color. For economy's sake I would probably ruler fold and either re-store in your totes or put on your shelves if you can. If you put in the totes - I would suggest labeling the totes with general color themes - greens; blues; reds; whatever. When you do your ruler fold or whichever method - label as close as possible to piece size and put a note on the piece. Might use up more pins/pieces of paper but would probably be valuable in the future. Re-mark that piece of paper as the fabric is used.
All of the above from someone who has no stash. But if I did, that's how I'd do it.