depending on your fusible and fabrics you can have trouble FMQ over appliqués. I try to do small test of any appliqués I do before doing a big piece.
Some things I've discovered are: I like Wonder Under or Misty fuse for fusible. If I think I might have trouble on multiple layer appliqué, I put a piece of batt behind the appliqué block first without the backing and put in some quilting or thread painting to kind of give it a trapunto look. I trim away under laying fabric from behind my appliqués after I have stitched the edge in satin stitch or buttonhole stitch. You can only trim away from under an appliqué if you "window" it. That is where you remove the fusible from the center of the fusible down to 1/4 inch inside the pencil line. You then iron the "window"to the back of the appliqué and cut it out for fusing. I have also found that some batiks with their tight weave are harder to FMQ through without skipping. Use a super sharp needle and keep the appliqués small so that you can quilt around the edge only if needed.