Its all up to you and how you want to quilt it.
As for quilting on applique, I have examples of antique applique quilts where it was quilted in an all over pattern and they went right throught the applique with no reqard for the applique design
Todays quilters tend to quilt around the applique first, then within the applique as it suits to add to the design.
Dresden quilts need to be quilted within the plate as it is too much unquilted space to just quilt around the outside and in the circle. I have seen two quilting designs that both do nicely. One is to quilt in the ditch between the panels and the other is to quilt 1/4 inch inside each one. Then a quilted design in the circle and of course the plain space between the plates.