I also have been successful in creating the ".packages" file, but no ".subpackage" file in the sub-pack folders.
The folders do exist outside of the parent folder with the Apogee pack. So you get the "Apogee" folder, "Apogee (Amber)" folder, "Apogee (Black)", "Apogee (Blue)", etc.
Mormegil uses the "Save package as individual icons" option in IconPackager\Settings category, which results in a folder with all icons available for copying to another folder (for say ObjectDock use).
The parent "Apogee" folder has icons, ".iconpackage" file, and the additional ".packages" file - while the sub-package folders have the icons that are different than the parent, and the ".subpackage" file only.
I have been able to create packages (which I save to the IconPackager\Themes sub-directory), and then assign them as sub-packages (and shows them in the drop-down list inside parent listing) - but this still leaves the packages which were added as sub-packages listed in the normal list as well. I have not found a way around this, nor how to create the ".subpackage" file - which I believe to be the key to the issue.
IMHO - An updated "Help" file is a must in this version. 