If it's just a small cuddle quilt I would not use batting, if you think the flannel is thin I'd use a layer of that as the batting. Since you are using cotton and flannel I would prewash all of it because the two types of fabric shrink differently. The flannel will shrink a lot and might need two washings.

I love making flannel quilts, and flannel backed quilts. I always use batting. I love how sort and snuggling they are

Your choice. I like the batting in the quilt because it makes them seem softer to me.

I back many quilts with flannel- I always use flannel- we like our quilts soft, warm & lofty