I organize ruler fold yardage (most of my stash) by dominant color. I do have several bolts (white and black) that I just leave on the bolt stored on a shelf with my other solids. Flannels and holiday are separate. I have very few bundles (fat, jelly, charms) but they are stored separately as well. I really need to figure out something for fat quarters as currently they are stored in a container with no rhyme or reason to it. I have smaller containers for spare squares and blocks (left overs).