There are several types of trapunto. The traditional trapunto was done by making a slit in the background fabric under a leaf or flower and bits of batting were stuffed in and then the backing was hand sewn shut. I like to do the method where I put a piece of 80/20 batt under my applique and stitch around the applique by machine. I then cut off the extra batting outside the stitching line and then sandwich my top as usual. I don't mind the 2 rows of stitching around my applique when I quilt it later but if you only want 1 row of stitching, you can do the first stitching around the applique with water soluble thread.
Geta does another method as posted above. YouTube probably has a bunch of videos, you will have to watch them to see which method you want.