What batting are you using? If it is a thick, or high loft batting, that might be causing the puckers. I have found that using needle punch cotton, such as Warm and Natural is the best for machine quilting. It is the perfect choice for spray basting.
Are you taping the backing fabric taut before layering? Not stretching it, but making sure it's just nice and flat and not wrinkled.
And pins are good. Saftey pins and then sometimes I also put some straight pins in if I'm sewing long straight lines.
There are lots of different things you can try. Maybe there's an experienced quilter that can help you layer your next quilt and give you some tips in person. There's nothing like in person and hands on instruction to make things go more smoothly and easier.