Sorting out scraps really does help out later when setting up a quick project or when needing that particular size or color to fill in for variety. I sort my 2 1/2" squares according to size and color.
A friend suggested using boxes from Ikea that have cardboard partitions to keep the squares separated and organized. When I went to buy some they were sold out so I looked around and saw that the wine boxes at the grocery/liquor stores had cardboard partitions to protect the bottles during shipping that were about 3.5" square - I asked if I could have a bunch of the bottle inserts ( took the ones that were not too thick/heavy cardboard) and then bought rectangular plastic containers from the dollar store. Better price than Ikea
I cut the partitions to fit the containers and now have my squares pressed & neatly stored. LOL I have a stack of boxes with squares sorted & ready close at hand.