I fold mine up and keep it in one of my sewing cupboards, usually in a bag so it doesn't attract lint or threads. I usually only buy what I need for a project though, so I don't have tons laying around. I do have lots of scraps however, which I keep in old batting bags or grocery bags in my sewing cupboard. Not the most organized system, but it works for me!
Just a suggestion - I thought many times about tossing some of my batting scraps because I wouldn't make enough items that small to use them, but then I discovered a trapunto technique that really helps use them up while adding dimension to my quilts. It's all done on your sewing machine before you even layer your quilt, no stuffing required. I learned from visiting Patsy Thompsons blog, and she even has a few instructional videos on YouTube if you're interested. :)