Amazing timing. I just finished my very first rag quilt, also done with the Accuquilt Go! I made it using three layers of flannel (Grinch Christmas fabrics on the front and back of the quilt and plain white flannel for the middle layer). Although I considered layering them together before cutting, I think it would have been very hard to roll it with three layers (you must have strong arms!!!). As it turned out, I was fussycutting the top layer so had to cut each of those squares separately anyway. It really wasn't too bad layering them after they were cut. Will try to attach a picture on a separate reply.
BTW, I had read that it's really important to wash your flannel in hot water in advance of cutting/making the quilt (hope I'm not too late with this suggestion). It will shrink a lot, and not at the same rate as your non-flannel fabric.