My Autopano Pro forum

Nope, in order to do that you should create a new layer, so now you will have 2 layers, the main one and the new one. Lets call the main one "base" and the new one "people". Base should contain your whole pano, and "people" should contain the extra photos of people and any other moving things (things that changed between shots). Now render using %L in your render name in the Render Settings dialog, so you will get 2 files, e.g.:
pano001_base.png
pano001_people.png

Here's an example of your source photos and layers:

[01][02][03][04][05][06][07][08][09]
[10]            [11]

01-09 are your base shots, 10 and 11 are extra shots with people.

In your graphics editor (Gimp, Photoshop, whatever), open the Base pano, add People as a layer, and use a mask to leave just the people without the background.

But now what to do if you have many people shots of the same angle, like this?

[01][02][03][04][05][06][07][08][09]
[10]            [11]
[12]
[13]
[14]

Di the same as above, using %L in the filename, but also enable the "Layers: embedded" option and render to a tiff or photoshop file. IMPORTANT! Save your pano before doing this, as enabling "layers : embedded" when you already have more than 1 layer can make APP crash.

You can do that too, but then you dont control the blending.