Go ahead and use cotton flannel. Make sure to wash & dry it twice before you use iit. It will shrink some the first wash and more the second wash. I found an adorable childs quilt in a thrift store, flannel backed. The flannel had not been pre-washed and shrunk so much that the quilt top was like a bowl.
I've also used a very light weight pellon iron on facing on flannel to stablize it and help it keep it's shape. Seems to have worked so far.