I think there's no customization for applications in the Whisker menu, it is just reading the .desktop files in /usr/share/applications
From what you have said above I think what I thought must be the Whiskers menu is not in fact the Whiskers menu. In the above are you describing as the Whiskers menu the one that opens when you click on "Applications" in the bottom left hand side of the desktop? If this is the case then Palemoon does appear under "Internet". I added under "Categories=" Network;WebBrowser;
to the .desktop file so that Palemoon would appear in the same category as Firefox. This is the menu that is very similar to those you see in the puppies with different desktops to that which r12 uses.
The one which I thought must be the Whiskers menu is the one at the top center of the desktop. It ends in a small circular blue icon which looks like a mouses head with whiskers hence the reason for me thinking it was the Whiskers menu. It is this one that I would like to be able to edit. I hope this post makes sense to you.
Regards,
Ken.