Terry, To find the correct settings for a fisheye sky shot, I suggest you shoot a test panorama consisting of a horizontal row of shots and one shot with the camera pointing upwards to capture the sky. The lens type should be specified as either circular fisheye (if the edge of the image circle is visible in the shots) or fullframe fisheye. For a circular fisheye, set the crop circle just inside the image circle in the shots. Note that all of your images should be presented to PTGui in the same orientation (all landscape or all portrait). The camera's auto rotate sensor does not give reliable results when the camera points directly up or down, so images can be produced in either orientation.
When the images have been aligned with PTGui and a satisfactory 360x180 panorama has been produced, all you need do is generate an output with only the sky shot present. To do this, enter Advanced mode via the button on the Project Assistant tab and select the Create Panorama tab. In the Include Images list, uncheck all the images except the sky shot.
John