Apart for ghosts and such, I use the keep/remove tool to have a photo fill the zenith and nadir, but not anything else. Unfortunately (other than editing the source image) there is no easy way to tell Autopano to only use that shot for the missing part and for nothing else. The only way to get it to do that is to spray 50-100 keep/remove points.
I suggest a polygonal mask instead of points. That way we can easily draw around the whole region we want to keep.
I also suggest an option "Use only where needed" on a photo. What that does is it will only use that photo for parts which no other photo covers, so I can add a nadir shot, set it to "use only where needed", and Autopano will use it only for the nadir hole plus a few pixels round the edges, to make a smooth transition. This is all currently possible with spraying the right amount of keep/remove points, but it would be much easier with these two tools: polygonal mask, and "use only where needed".