As Geri said, you can do either. I am doing an applique BOM and plan to trapunto certain areas. I am doing the hand applique first, then before I quilt it, I will put a piece of batting under the area I want raised and machine stitch with invisible thread as close to my applique as I can get it, then turn it over and trim the batting away as close to the stitching as possible. Then I will layer and quilt.
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