Hi Thomas,
To use an other instance of menu bar, you'll have to edit
file
header_menu.php.
Starting at comment <!-- main menu -->, you'll see a "mainmenu"
section containing menu's first level items. Create a new one below it
and name it "mainmenu2" for example. Take care of
rel="..." options
(ex sub_recent) as it correspond to sub items sections.
Finally, in each page you have to modify your menu call to
add a new instance of dropdown menu script, as this:
tabdropdown.init("mainmenu", 0)
tabdropdown.init("mainmenu2", 0)
I haven't tested these... so take backup files before edition!

Regards,
Jacques