Here's a basic process.

1)  Line up the source and target actors as well as possible in the 3D view.  This may involve any or all of the transforms, as well as morphing or using deformers. 
2)  Start the script.  Select source and target actors.
3)  For complex meshes with ovelapping or internal geometry, such as heads, it may be best to use the materials screening option.
4)  One may also wish to use region box screening to restrict an area of comparison (I've done this with the ears, above).
5)  Analyze the meshes.
6)  Transfer morph and transfer shape produce somewhat different results.  Try using either to see which one may be best for your needs.  When running transfer morph, a morph needs to be selected in the listbox.  When running transfer shape, the desired morph (shape) needs to be set on the source actor.
7)  In cases where materials or regions were screened, more than one comparison will need to be run for the meshes, to catch all the verts, eventually.  This is the "lather, rinse, repeat" step.
8)  Once you have a good series of datafiles for actors which were screened, you can merge them into a single datafile using the merge option in the file menu.
9)  Smoothing (and the other "extra" functions) work on the source listbox selection - or, more specifically, on the selected morph for the source actor selection.  All of the extra functions also require that both a source and a target actor be selected. 

I'm sure I've left something out.  That covers the basics....

===========================sigline======================================================

Cage can be an opinionated jerk who posts without thinking.  He apologizes for this.  He's honestly not trying to be a turkeyhead.

Cage had some freebies, compatible with Poser 11 and below.  His Python scripts were saved at archive.org, along with the rest of the Morphography site, where they were hosted.