I keep most of my scrap pieces inside the largest size "leftover" in the bunch folded up in the main body of my stash. That way if I want to use that fabric again all of it is together.
I have a section set aside for 2-1/2" strips that don't also have larger pieces.
If there's not a fairly good size piece left then the little bits go into either a light or dark colors bag. Unless it's seasonal then I have a separate one for those.
And I have a bag of tiny stuff that can be used for stuffing pillows etc.
This is working for me so far.