I confess that I do not study the art of doll making, so I've been experimenting in adding a little more depth. Here's the method that has worked best for me. I embroider the features and then put the doll together and stuff it. Then I go back in and pull the eyes back by taking a stitch behind the embroidery. It's kind of tricky because you can't catch any of the embroidery in your stitch and you want to get the embroidery out of the way without damaging it.
The result is subtle.
But I think it gives the face that extra something. What do you think? Success?
I can see how the old school way of making dolls and stuffed animals with shoe buttons eye (like Raggedy Ann), would be simpler. You just pull the button tightly when you attach it so that it pulls back into the face.