It's a personal choice. I have a quilt that is flannel back, flannel top, with W&N batting in the middle - and it's the most popular quilt in my house. On the flip side, I know quilters who only use 2 layers and are perfectly happy.
You could try spreading out 2 layers of flannel on your lap as you sit on the couch, then add a third layer and see how much heavier it is. This won't be the same weight as your rag quilt, because a pieced top will weigh more, but it will give you an idea of how much added weight will be in the quilt if you add a middle layer.