Aside from prewashing (I wash and dry in the dryer twice), I heavily starch flannels before cutting. This stabilizes it so it doesn't stretch out of shape with handling.
The process I use is (1) mix a 1:1 solution of Sta-Flo liquid laundry starch and water, (2) apply to fabric with a large wall painting brush, (3) when fabric is saturated I toss it in the dryer, and (4) iron with steam. This leaves the flannel with the stiffness of light cardstock -- very stable for precise cutting and piecing.
It's a good idea to use 1/2-inch seams with flannel too.
Since your pieces are already cut out, you might want to make a rag quilt out of them instead of the usual pieced quilt.