I use flannel a lot. Wash/dry, wash/dry. Also use a wider seam on back, like half inch. Even better, use a serger. Flannel likes to fray a lot.
You can use however many layers you want. Your quilt, your rules. I made my DH a t-shirt quilt and used warm and natural in the center and backed it with flannel. It's very warm - too warm for the south. I have done quilts with flannel instead of batting and backed it with flannel - that works better for me. I like to anchor down all the seams with quilting.
One of my grandmothers used to make tops and only use a sheet for backing and nothing inbetween - everybody loved them.
Let us know what you decide.