I have decided that I want my machine appliqué stitches to show, instead of trying to achieve an invisible stitch by just taking a small bite of the cloth. I have used my elna point-de-Paris stitch cam and thread to enhance, not necessarily match, the pieces appliquéd down.
Denise Sheehan suggests tightening your bobbin tension to keep the color of the bottom thread from pulling through onto the top. I am lucky that my elna has a small dial to do just this adjustment. You can see the top thread has actually been pulled through to the back--this ensures that the top thread color will be neat and even. I also pull the threads through to the back at the beginning and ending of each stop and start and knot them, cutting them just past the knot. This keeps the back not only neat, but doesn't allow any tangles or extra bulk. I do not cut the excess backing behind the appliquéd pieces--I do not think it is necessary.