When I made flannel rag quilts for babies or young kids I didn't put any batting in the middle, the two layers of flannel were heavy enough for such young children.
After putting squares together and snipping the exposed edges you should wash the quilt and dry it in the the dryer to remove loose threads and fuzz, this softens the quilt so nicely. Make sure you clean your dryer's lint trap, it will be full of lint.
May in Jersey