When I pieced a flannel quilt, I first washed and machine dried it twice to shrink it.
Next, I *heavily* starched the flannel. My method was to use a 1:1 solution of Sta-Flo liquid laundry starch and water. I painted this onto the yardage with a large wall painting brush, let the fabric absorb the solution for a couple of minutes, then tossed in the dryer and finished by ironing with steam. Only then did I cut the pieces. Heavy starching ensures greater accuracy with both the cutting and piecing of flannel because it stabilizes the fabric; doesn't wiggle around anymore.
It's also a good idea to piece with larger seams than the usual scant 1/4". If the pattern permits, moving up to 3/8" or even 1/2" is a good idea. This is because flannel tends to ravel more easily than regular quilting fabric.
If your pieces are already cut, you can still spray starch to add a little stability.
Oh, and be sure to clean your machine regularly while sewing flannel. It produces a lot of lint!