I haven't done it yet, but the embellishment book I have (by Rose Hughes) says to do the embellishment after the regular quilting. For sequins, bury the knot, come up where you want the sequin to be, then go thru' a small seed bead to hold it in place, and back down thru' the sequin & on to the next one. I can't remember what thread she recommended, if it was special beading thread or ??
Hope this helps! :D