Wash in hot water and dry at least twice to shrink as much as possible BEFORE cutting. Quilt heavily, as flannel doesn't have the memory of cotton (it sags where not quilted).
Otherwise, treat like cotton...starch to keep bias edges from stretching (although you will not get the material a great deal stiffer).
You may not need to add batting if you use flannel for top and back...it depends on how heavy a quilt you wish to make.
Good luck!