Can you post a picture of the design? Applique with embroidery is easy.
1. Hoop a stabilizer and backing fabric.
2. An outline of the first fabric is embroidered.
3. lay the first fabric on the outline, making sure it is big enough to cover the outline by at least a 1/4 to 1/2 inch.
4. Stitch the fabric down.
5. Remove the hoop from the machine, but do NOT remove the design from the hoop
6. Cut around the stitches as close as possible but not into the stitches.
7. Put the hoop back on the machine and stitch the decorative stitches.
This process happens repeatedly for each little piece. It comes out beautifully! Sometimes it helps to use a little water soluble glue to help hold the fabrics while they get stitched down, but I just usually use my fingers to hold it in place.
If the entire design is bigger than your hoop, then that's multi-hooping which is a bit more involved. Let us know.