if your using the same type of flannel, as in from the same store and section (not mixing quilt/ crafting with apparel) Washing shouldn't be needed. They'll shrink together in the first wash. If you wash it before hand it will start to ravel and you'll loose the little bit of stiffening agent the manufacturers use to make the cutting easier. Then it could be a pain. If your just using flannel from bits of shirts, those have been washed already and they'll be fine too. But if your going to add other types of fabrics, ie; cotton or silkies, I'd wash them all.
Rather than that, flannel is alot of fun to work with. Less pins needed to make it behave. Have fun. Hope it goes well ^_^