A friend of mine quilted an embellished quilt. He did quite a bit of embellishing, but I do remember he put the beads and "flat to the surface" embellishments on first, and then covered them up with a bright blue painter's tape so when he went to quilt it (on just his home machine), the solid embellishments were perfectly highlighted, and this kept him away from them while quilting. He also did a bit of hand stitching of motifs on it after it was quilted, and for this, he didn't let the stitch go through to the back, and sometimes the motif covered up a bit of quilting. Anyway, the whole quilt was just awesome!
If you were sending it out to a long arm quilter, I'd check with her/him before I added embellishments, just to see how they would (or could) handle an embellished top.