Prewash. Prewash. Prewash.
Actually, some people do wash their flannels more than once before cutting them to get as much shrinkage out of them as possible.
If you are cutting strips, I think it would be helpful to cut them on the way that has less stretch - usually the lengthwise grain that is parallel to the selvage.
So when you sew the strips together, they might "play" better together.
Also, depending on your flannel, make wider/deeper seams than 1/4 inch.
The lighter/flimsier the flannel, the deeper the seam. Minimizes the chance of the seams pulling apart.