I, too, like flannel backs especially on quilts for "littles". The walking foot is almost a necessity. Usually I do stitch in the ditch to stabilize the blocks before doing any sort of decorative thing. (I wish they'd come out with a stitch in the ditch walking foot! Could really use that one.) I always start with the grain of the flannel on the straight and in the middle of the top or bottom working toward the sides with all of those stitching lines going the same direction. Then do the crosswise. When crossing those lines of stitching that were done on the straight, tug just a bit on the sandwich so it will stretch with the crosswise grain and work those puckers out. This will work on the little puckers, not excessive ones, which actually should not be there if you started out with the back perfectly flat. If you work on a table, try taping the back out so it is smooth when creating the sandwich. It sounds like your back may be sliding without you noticing.
Salemm asked about using a flannel blanket as batting. I did that on one of my first quilts and wish I hadn't. It is one that was for my younger daughter and the blocks were all embroidered--a lot of work. I wish I'd used a traditional batt in that one. My opinion--depends on the use for the quilt. If it's for utility, good idea. If it's for a treasure, use a traditional batt. Flannel blankets work well for batting in a rag quilt as it is extra warmth and adds to the fringe.