flannel is pretty warm! i would definitly not use 2 layers of flannel. a low-loft cotton batting (like mountain mist or hobbs select) is a good choice- the cotton breaths- it is lightweight- low loft will add some body without weight/warmth- and a regular cotton backing-
even if you choose a flannel backing i would either skip the batting - use a lightweight/low-loft cotton batting- or use a layer of muslin- but using 2 layers of flannel will make it quite heavy & very warm.