I've followed these instructions succesfully (for I had the same problem as jasonkimmings), but unfortunately Autopano chooses the darkest exposure bracket for setting controll points, so they are hard to confirm or to reposite. Can I determine which bracket to use for controll points?
Welcome to the forum...
Yes, you can you can select the index level which will be used for CP detection - see screenshot 1
Second issue: Though I proceeded like described above and only one bracket got controll points, the different layers sometimes showed little differences in output and were superimposable only at first glance. I never experienced this using Hugin.
Why are you generating separate layers? If you do that antighost cannot operate can it?
As I understand it the seams will/may vary in different layers due to the way APG works.