I agree about glue basting your seams to get them to match. I take the work to my ironing board, line up the seams as I want them, then put just a tiny dot of Elmer's washable white glue in the seam line. Fix in place with a hot iron. The glue will wash out later, or a drop of water on your fingertip is enough to soften the glue to let you open up the seam.
To help with the puckering when quilting, I recommend heavily starching the backing fabric before layering. I use a 1:1 solution of Sta-Flo liquid laundry starch and water, "paint" it on the yardage with a large wallpainting brush until the fabric is saturated, toss in dryer, then iron with steam. I also spray starch the top. Starch adds stability and helps keep the fabrics from moving as you sew.
I do wonder if your sewing machine is causing some of the puckering. Having your stitch length too short can be a problem, an old needle can be a problem, and sometimes a rough area around the needle hole can cause a problem. (The latter can be smoothed away with emergy cloth or extremely fine sandpaper.)
When sewing on the binding, I do it differently. Instead of cutting the quilt, I use a Sharpie permanent marker to mark where the quilt will be cut. Then I sew the binding on, lining up the raw edge of the binding with the Sharpie mark. I don't cut the quilt until after the binding is sewn on. At that time, if I need to, I can adjust the cutting line slightly to make sure the binding is going to roll over to the back and end where I want it. I can cut the quilt a little larger than my marking first, to see how the binding rolls, before deciding on exactly where the cut should be (because I can always cut again closer to the raw edge of the binding or even, if I dare, shave off a little of the binding if the batting is too thick for a good roll).
Have you seen Leah Day's video on attaching binding by machine? Even if you complete the binding by hand, it's worth watching for her tips. Here is a link to her binding videos:
http://www.youtube.com/watch?v=wprg5vzkuGw
http://www.youtube.com/watch?v=7MRfA...eature=related