When mixing types of fabric, I always try to remembr to "respect the nature of the fabric" If you do use 1/4" seams besure you have a full 1/4" seam. It is so easy for the fabric to crawl. I have made crazy patch blocks with flannel on muslin and it worked. Shorter stitch will help. Minimal quilting usually in the ditch worked for me.
Making sure of the consistency of the seam allowance is most important. Since you have a heavier fabric to deal with I would use a thinner muslin for foundation. Good washing before to make sure it doesn't shrink further in use.