I have seen applique quilts with all over pantograph quilting, ones with echo quilting, ones with cross hatch lines that stop/start at the edges of the appliques... How ever you want to do it is OK, it is your project. You could draw your quilting design on clear plastic and lay it on the quilt to see how it looks, and (I recommend) making an applique block, sandwich it and practice on it to see if it turns out the way you want, or is difficult, work out any problems before working at the quilt