Hi Lars,
You could install Extended Menu for Joomla and publish it in User 1 instead of Main Menu. Extended menu allows for sub menus and is much more flexible than the default Main Menu module for Joomla. All you do is install the Extended Menu module and use it instead of main menu.
http://extensions.joomla.org/component/
option,com_mtree/task,viewlink/link_id,163/
Itemid,35/Regarding Transmenu for the Main Menu position - this won't work with the template asit is now - I could look at modifying it for you.
The issue is that all the DIV's in the layout that contain the DIV with the Transmeu have to have position STATIC for the transmenu to function properly.
I'll have to think about how to do that because currently that left column is floated and it would require a major rework of the code...
Hope this helps