I think there are vendors on Etsy.com that will make custom labels.
I usually use a pigma pen, but have done hand embroidery. On one of my first quilts, I used a sharpie, and it faded a lot. But before you use pigma pens, test them for washability. I have had no trouble with black, but I bought a pack of bright colors and pre-tested them on muslin. Some of them ran and transfered to other fabrics, so I haven't used them on my quilts.
Usually my label is in bottom right corner of the back, but I've put labels in other spots on the back - once to cover up a stain, once to cover up a slash I made when cutting the loose threads away. I've also put one in the bottom center of the back. I don't really think about it much.