Hi roefie,

Simple answer - yes, you should be able to achieve this. it doesn't matter that the index page is outside of Joomla.

I see that you are using SEF URLs - perhaps sh404SEF? And the site isn't finished, so it's a little hard to see what the site structure is.

One of the easiest ways to structure this might be if you had a separate Joomla Menu set up for each main section of the site. e.g. one called "mainmenu1" with all the links & site structure for your 1st image, then "mainmenu2" for links & site structure for your 2nd image, etc.

Then in MetaTemplate Pro, just assign your 1st template to mainmenu1, 2nd to mainmenu2, etc.

There would be other ways to achieve this too, but it depends on your site structure.

Hope this gets you started,
Stephen