I have the same problems. I think I enjoy quilting too much to take so much time to do it perfect. I want to create and not spend months doing it.
However, I have found a product that helps when putting the layers together and quilting thorugh them.
It is a adhesive spray. Completely repositionable. disappears after first washing, but holds layers together well enough that they don't shift while you are quilting (even machine quilting)