The nice thing is, it's your quilt and you can make it however you like, and you have gotten great advice so far. I'd just like to add that if you use flannel it should be pre-washed as it tends to shrink alot. You said you are new to quilting, but if you have some scraps to play with make three small blocks, one without any batting, one with batting and one with flannel.
Lastly....welcome to the quilt board you'll find many friendly and helpful people here!
