There is a book called Quilting in Sections, by Marty Michell that has a few different methods. I tried out a few sample sized pieces from her book and liked the results of the "low fat" method best. In that one, you lay out your backing/batting/top as usual, baste the center, then fold back the top and back and trim the batting into halves or thirds, whichever works best for your quilt. Then you are working with less bulk. Once you quilt what's left, you piece the batting back together and quilt the remainder.
http://www.amazon.com/Machine-Quilti.../dp/B000NNGZJE