I think if you piece first and then wash the backing, you will get a lot of unwanted distortion if the flannel shrinks. Not all flannel shrinks, and different flannels shrink in different amounts in different directions.
I would actually recommend piecing the flannel back and Not pre washing IF you will be using a moderate amount of quilting. Quilting will prevent fabrics from shrinking too unevenly, as the batting prevents any one piece from shrinking too much. However this won't work if quilting lines are too far apart. I would estimate you want quilting lines no more than 3" or so apart for an unwashed flannel batting.