I've never bought a fat quarter. I tend to make large quilts, so my requirements for purchasing are: that it be on sale or that I can use a coupon; that it be quality fabric that I can't see through; and that I really love the print and color(s). I usually buy the rest of the bolt, which is sometimes a lot and sometimes not. I generally do not buy anything less than a yard.
I store my fabrics (on shelves) by what goes well together in a quilt. There's also a stack of mavericks that don't seem to quite match anything. I keep snippets of the unmatched ones in an envelope in my purse, so that when I'm browsing at the fabric store, I always have them with me in case I'm lucky enough to find matches. I always do, eventually. There are days that the shopping gods look favorably upon me and I come home with excellent additions to my stash and other days ... nothing!
I never worry about having too much of one fabric because I know it will eventually be used, nor do I keep track of how much is left or how much I have of any fabric. Once I choose a quilt project and the fabrics from my stash that I think are right for that quilt, then I measure each piece. If have don't have enough of a chosen fabric and can't find another in my stash with which to replace it, I don't live far from the fabric stores.
This probably doesn't sound very organized, but it has worked well for me for many years.