I do both things. I have a stash that combines my fat quarters and yardage by color; but, I also have things by project. I use "project envelopes" that I picked up at walmart or target, etc... they are clear or tinted plastic. I label the envelope with pertinent info, put the pattern inside, along with fabric I pull from my stash. I set the envelope atop of the yardage that won't fit inside and keep it all in a rubbermaid drawer until I'm ready. I also list these future projects on a whiteboard, so I don't worry about them. It's a handy system for me and when I'm working on those projects, the pieces, scraps, my notes, and baggies of blocks have a "home."