not sure exactly what you mean...
do you just want to use flannel for the back of a baby quilt? without batting? if so, you can put it together pillow-case style (put right sides together and stitch around 3 sides, turn right side out, do some quilting lines on it, close the 4th side and stitch closed, top stitch all the way around the top.
or you can do it the usual quilt sandwith way, put the two layers together wrong sides together, quilt it and bind it.