I do a lot of embroidery in my quilts and ALWAYS do it before it is sandwiched and quilted. I used a machine to embroider and there is no way to make it just go through the top layer, when you embroider it will go through all layers. Me maws quilt that I did recently, not until it was almost done quilting did the men in my house decide it had to have names on all the corners, so the names were done after quilting and I do not like it. Its not that noticable because I used white bobbin thread but I know its there and do not care for the look of it.