I was able to figure it out by being persistent. My model is actually very simple, it's made of 3 vertex meshes. One the body and two and three the eyes. The problem that I am still having is that some joints are not oriented properly. The command dose a decent guess, but it's only a guess, is their a way that when placing the bones, that they are oriented in a predictable fashion. I guess I will need to experiment, but my guess is it depends on what plain you place the bone, it will orient it to that plain? Mainly I will be using Axis joints and a couple of ball joints on the shoulders neck and tail. Any insight you my have will help me a bunch.