My quilts usually "talks" to me and tells me how it wants or needs to be quilted. Not by any general rule, but what I have done in the past is that if the applique is big and made with a printed design, I quilt over it, but never with the same quilting design as the rest of the quilt, but with a very different design that makes it jump apart from the rest of the quilt. If the applique is small or with a more plain fabric, I usually quilt around it. In general, listen to the quilt. No rule of thumb.