My personal opinion of flannel is I do not like doing any type of quilting on it so I try to not use it but there comes times when you have to and then you must make the best of it. I find flannel stretches lots so I use 505 Spray Basting to hold the backing to my Hobbs 80/20 batting and then I spray the front to the batting. I add some pin basting to keep everything in place and believe me nothing moves. When you are done quilting, you can wash your quilt or hang it on the line to air freshen. The spray bast evaporates when exposed to air.
There will certainly be other solutions given by many experts on this forum. I just know this is one solution that works.