It would be very helpful in a number of cases to be able to tag a specific image to be pulled to the top when stitched, and another segment of another image is used. Further explanations and an stitched result are provided in your other forum at
Besides multilayered result files (where, using an image editor, you can decide afterward which of several images must contribute to the resulting pano by using masks) and masked TIFF source images (not appropriate because no control point is set in the masked areas) there are no 'top' nor 'bottom' source images in Autopano.
I believe this would not be possible because to decide which of the overlapping source images is to be used, Autopano would need precise instructions (in your example it should know where are the boundaries between the sky and the ground.)
About your example: you should have a look at Enfuse or Tufuse (in Autopano forum or elsewhere using Google) which is helpful for combining source images of varying exposures even when two full sets of source images were not recorded.