As soon as i'm done cutting the batting I measure and put it back in the same bag. I check the bag to see if there are other scraps that need to be stitched together. A quick zigzag stitch down the seam keeps it in check.

I measure, write the measurement on a scrap of paper, staple it to the batting and put them in numbered clear plastic bins. I also list them on a spreadsheet, l can tell very quickly which bin to go to in order to get the one I need.