I have done a hand appliqué on a Double Irish Chain and done machine embroidery in the block next to a 9 patch. With the appliqué it was after the block was put together, because it was just a hearth in the center. It was not a problem but the machine embroidery I used a larger piece of fabric and cut it down. Mainly because I am not great at centering the embroidery and 2, I was concerned about the embroidery shrinking the fabric.