You can definitely do a quilt in sections. There are a variety of ways to do this, including one that cannot be discerned after the quilt is finished (splitting the batting into 3 sections, quilting the middle, then re-attaching the batting sections to quilt the sides). Here is a link to a book that explains the different ways of doing this:
http://www.amazon.com/Machine-Quilti...dp/B000NNGZJE/