I always prewash flannel because some of it shrinks a *lot*, and it does ravel more than other cottons.
When I worked with flannel, I followed Sandy Bonsib's advice and used 1/2-inch seams rather than 1/4-inch seams. Also, I starched the flannels heavily before cutting, to stabilize them. Both of these helped make perfect joins. Flannel has a tendency to move around a lot when you are sewing it, and starch really helps with that.
I prewashed and dried the flannel, then "painted" it with a 1:1 solution of liquid Sta-Flo starch and water, tossed the fabric in the dryer, and ironed it with steam. This made it perfectly stable for cutting. The 1/2-inch seams are a good idea because flannel is relatively loosely woven; it prevents the seams from pulling apart later because of frays.