If you're planning to piece the flannel (instead of making a rag quilt), I highly recommend heavily starching the flannel before cutting. It stabilizes it so it doesn't stretch or distort on you while cutting and piecing.
My starching method is easy. I just mix up a 1:1 solution of Sta-Flo liquid laundry starch and water, "paint" the solution on with a large wall painting brush until fabric is saturated, toss in dryer, and iron with steam. Flannel comes out pretty stiff this way, similar to lightweight cardstock, and is *not* going to stretch on you. Of course you need to wash the quilt before giving it to someone!
Depending on the pattern, I also like to use 1/2" seams with flannel because of the potential for fraying.