I used flannel for a back on a baby quilt and then quilted on my longarm using rulers for some of the design. I found that the ruler with the ruler base caused quite a change in the tension and was somewhat difficult. I would try a sample first before quilting if you are using rulers and base.
I always prewash all fabrics and put them in the dryer. If the entire quilt (top and backing) is a similar flannel, you may not have a problem if you do not prewash.