Here's a trick I use to get my backing straight with the front when I glue baste but it would work with pinning and thread basting as well.
First piece your back making sure it is larger than the front but a few inches all around. Pick a seam that is going to be your reference point somewhere near the middle third of the backing. Tape drinking straws or unsharpened pencils along the seam on the right side of the fabric. I use painters tape to do this. When I glue baste I do this after I glue the batting onto the backing. If you were pin or thread basting you would do it before you sandwiched the three layers together.
Next, with right side of the backing facing down, layer your top on (or if you are pin or thread basting your batting, and top). You will be able to feel where the seam is thanks to the straws/pencils. Match this up with a straight reference point on the front of your quilt. Voila! your back and front are straight together and the quilting, especially if you use straight line quilting will look much better.