Andrea,
I put the latest Manual update on the website and it only has one Glossary and then the List of Tables/Figures and finally the Index. I was able to use the index from there. Entries for the Index are simply next to an item as \index{phrase you want to go into the index} . You can see an example in Plugins.tex for Motion51. So I do not know why you would be getting 2 glossaries but maybe it is because of running "makeindex" twice? and maybe there is a way to make it create both the Glossary and the index at the same time?
Also, updated releasenotes.pdf to reflect the Prores improvements you made that were checked into GIT today.