The stipple would come first. Then stitch down the die line which will show where your applique would go. Then you place the applique fabric and stitch it down. I don't use wss on applique unless I have added a name and it goes at the end of the entire process.
OR maybe I don't understand your question?
well I have added elements to the placemat stipple the background then the applique design & then a filled design too