I have some of the hard plastic see through bins with individual holders for each spool that I bought at Joanns at 75%off. They are tooooo expensive to buy here in Canada. The other thing I use for spools, material, projects, scraps(labelled by size etc) are the plastic containers that lettuce and strawberries etc come in from Costco. They hold well, are see through and stack great.
I store everything in them. Extra untensils for a crowd, cookie cutters, everything is separate and visible instead of being at the bottom of a cupboard. Also, I have a neverending supply because I just keep buying lettuce and stuff.