I have not yet organized my stash (it's on the to-do list) but I know how I'm going to do it. I know I don't want bins. Just don't like them. I want shelves and I want to put my fabric on boards and stand them on the shelves.
The FQ's will be folded though and shelved.
So ... if I have an FQ that matches some of my yardage, I will pin a post it note to the FQ and the yardage piece that reads "see also yardage" or "see also FQ". That will remind me when I'm old and dotty that I have another piece of it somewhere.