First I iron the pcs I intend to keep. I then cut several sizes of squares from them. The large pcs are cut into six inches, then on down the line. If the pc is very large, say a full fat quarter, or near to it, then I just fold it and put it into a plastic shoe-box sized container, already sorted by color.
For the cut pcs, I put them into a separate container by size and go from there. I have found that having the squares already cut into sizes - say about 3 inch - somehow makes it so much easier to actually set out to make a scrappy - I love nine-patches but I have a bunch of four-patches that I make every so often - soon I'll have enough to make a quilt. I just finished a small nine-patch top I'll quilt for a new baby when ever one appears in my life from where ever. This one I made with 2-1/2 in. squares.
There is one down side to this. I will never finish using these scraps if I live to be 150 and never buy another fat quarter again. I also donate bunches of already cut 6 inch squares to others to make for Project Linus.