It starts all the way back in Modeler. The trick is to make your object with its long axis lined up with the Z-axis in Modeler. When you save an object in Modeler and then load it into Layout, the objects position and its orientation are remembered. For example, if you model your space alien on his back he will be loaded into Layout in the same position, on his back. They too are added along the Z-axis.
Lets look at an example.
Below is a picture of a flour sack in modeler. When this is loaded into Layout it will keep this orientation. Here is the sack loaded into Layout. I added one bone to demonstrate the default position of the added bone. This makes the process of building the skeleton much easier.