flannel is a bit heavier/loftier than regular cottons (normally) starch helps- and you have to baste well---lengthen your stitch length a bit- put together a small (like a 12" square) practice piece and try different stitches, and basting, practice until you find what works for you (you didn't say how you were quilting it- i'm assuming machine...did you use a walking foot or a free motion foot? what about batting? there could be many reasons for your problem- maybe show us some pictures of the quilting/puckering??
tell us how you basted- what foot you are using- what batting (loft/weight) the loftier the quilt sandwich the more chance of puckering- unless you really lengthen the stitch length- and if possible lessen the pressure from the foot (some machines you can adjust that-some you can not) if your machine has settings for light/medium/heavy fabrics- set it for heavy *that will lighten the foot pressure*
practice on a practice piece---preferably with the same combination as the quilt) until you have it the way you want it---then move on to your quilt
starching the flannels will help them be more manageable....and more information may get you more advice.