As Prism99 said, no rules. However, I would applique first (you don't want stitches showing on the back side of a finished quilt. If I got it to do the quilting (longarm), I would do an echo around the appliqueing, then crosshatching out from that point. I do NOT like seeing the appliqueing ruined by someone quilting over it --- I think it detracts from the hard work that was done!