When first realizing you need to organize your space, you probably are getting a pretty good stash. First separate out any fabric that you'd use for regular sewing & not for quilting, like polyesters or silkies. Those need to always stay away. Then I'd go for separating out either by color groups or print types, like calicos, reproductions or batiks. That should get you started. Whatever system you use, realize that it will need to be flexible & change over time.