I usually use a larger pattern with fewer pieces when quilting with flannel. I also cut my pieces with a rotary cutter with a pinking blade. I also use a larger seam allowance and longer stitch length. Just my preference. :-D
Oh, and prewash, prewash well! I pink my cut edges before washing yardage and threads are kept at a minimum. Also pewashing does not necessarily mean you have to aggetate the heck out of the fabric, I prewash fabric on the delicate cycle using the same temperature water I would wash normally.