I enjoy hand applique more, but you could really do either depending on what type of finish you're seeking. Just make sure the top is pressed well -- especially in the area you plan to applique -- before you start. Check the seams to make sure they are either pressed open or completely pressed to one side; go slowly & double check seams before feeding them through your machine or hand sewing needle to make sure they are laying properly. You should be fine. People have been sewing applique on top of patchwork for as long as there have been accidental holes. How much more fun it is to applique on top of patchwork on purpose!