I've made several quilts combining cotton and flannel. I've used a 3/8 in. seam allowance. Of course, this might not work out for a complex quilt pattern, but mine are usually a combination of plain squares and four-patches, or plain squares and HST's. Both cotton and flannel were pre-washed, and I've never had different rates of shrinkage when washing the finished quilt. I love having that extra little bit of seam allowance when pressing.