I would prewash and dry flannel at least once (some people do it twice) to tighten up the weave. It usually shrinks a lot.
When working with flannel I also apply heavy starch to stabilize it so it doesn't stretch while sewing. My method is to mix a 1:1 solution of Sta-Flo liquid starch with water, lay the fabric out on my kitchen island, and "paint" the starch on the fabric with a large wall painting paintbrush. When the fabric is saturated, I throw it in the dryer and afterwards iron it with steam. It sounds like a lot more work than it is; I actually don't mind doing this. The flannel comes out quite stiff and I can then cut and sew without any worries about stretching. The starch comes out in the first wash.