I heavily starch my backing fabric before layering. This stabilizes the fabric so it is much less likely to pucker when machine quilting. My method is to mix a 1:1 solution of Sta-Flo liquid laundry starch and water, "paint" this solution on with a large wall painting brush until the fabric is saturated, toss in dryer, and iron with steam.
Also, in my experience spray basting does a better job of preventing puckers than pinning ever did for me. I think this is because spray basting keeps the layers continuously "stuck" to each other; with pinning the "stuck" parts are 4 inches or so apart.