You do not want to prewash a top without first basting it to a foundation fabric, even if you are handwashing; otherwise you risk a lot of distortion. It would also be a good idea to block the top, complete with foundation fabric, while it is still very damp.
If quilting and not tying, I would skip washing the top and just be sure the flannel is preshrunk. Poly batting does not shrink, so quilting fairly closely will also keep the fabrics from shinking. Most cotton battings shrink about 3%, which gives the nice crinkling effect I like.
If the quilt will be tied rather than quilted, uneven shrinkage of fabrics can become a problem. In that case I might go to the trouble of prewashing the top.