I agree with starching the flannel backing before layering. My method is to mix a 1:1 solution of Sta-Flo liquid laundry starch and water, "paint" this onto the yardage using a large wall painting brush, wait a couple of minutes to make sure all the fibers are saturated with starch, toss in dryer, then iron with steam. This stiffens the flannel quite a lot, which means it will not move around on you or pucker while you are basting and/or machine quilting. It's a good idea to starch the top before layering as well. Layers of spray starch help, although it will never get as stiff as the Sta-Flo solution.
I think the Elmer's glue would work fine with flannel. The glue is actually just at thicker form of starch.