Spray basting really helps because it connects all three layers at all points of the surfaces. Pins, in contrast, are connecting the layers only every 4" or so.
Another thing that really helps to prevent puckers on the back is to heavily starch the backing fabric before layering. This stabilizes the backing fabric so it doesn't stretch and is less likely to fold over on itself. My method is to mix a 1:1 solution of Sta-Flo liquid laundry starch and water, "paint" this on the yardage with a large wall painting brush until the fabric is saturated, allow a minute or two for the starch to be absorbed, toss in the dryer, then iron with steam. The fabric comes out pretty stiff. It is much easier to sew a pucker into soft fabric than into stiff fabric.