choose a good batting- i've made tons of flannel quilts- seldom pre-wash my flannels- use flannel on the backs of most quilts- they come out beautifully! as long as you follow the recommendations for quilting on the batting package you will not have any (lumpy mess)
read the package- some batts (like warm & natural) allow up to 10" between quilting lines- this is the batting i use most often for all flannel quilts- but i have used hobbs 80/20 heirloom, dream wool, dream green, and bamboo for flannel quilts and all of them have come out wonderfully- and many have been through years of washing/drying-
as long as your materials are good quality materials and you follow the recommendations it will be fine (if the batting says quilt every 2" and you only quilt every 6" you will have a lumpy-unhappy quilt)