I heavily starch my backings to prevent puckers while FMQing. That and spray starching eliminate the problem for me. Even heavy starch does not interfere with pooling the quilt during FMQ; the starch breaks down a little as you handle it.
Sharon Schamber has Youtube videos demonstrating how she resizes skewed blocks to true. Basically she wets the fabric with spray starch, pins it to shape, and irons. Although she is doing it on individual blocks, using spray sizing on your quilt top should help with some of the distortion issues, including helping to flatten areas that are a little poofed out.
Here are links to some of the Sharon Schamber videos:
http://www.youtube.com/watch?v=v-3RIWhBvcA
http://www.youtube.com/watch?v=i6aplw_tVZc
http://www.youtube.com/watch?v=lIjZqABo2NY
http://www.youtube.com/watch?v=sQkF02vpVuw