I agree with the others. Also, having learned this the hard way ... be sure to pre-wash your flannel in whatever laundering conditions the final recipient will use. Pre-washing in cold water/low heat does no good if your recipient then washes in hot water & dries on high heat. The flannel will shrink like crazy & the plain cotton fabric will crinkle a lot to compensate.
Flannel will stretch more readily than quilter's cotton. I take extra care in squaring up fabric, starch heavily & do extra basting when combining the two. I also find for piecing, putting the flannel on the bottom helps to ease in any little bit of extra fullness that may occur while moving through my machine.