Ok ... why don't you actually install (move) WB into a subfolder and let the script reside in the root?
How did you manage the menu? Did you use Ryans script or do you use the show menu function like this here:
<?php show_menu(1,1,-1);?>
basically it shows only the menu below the first sublevel (everything which is under EN, DE, etc ...)
also the language selection can be made with a 2nd menu showing only the top level:
<?php show_menu(2,0,0);?>
but for this you need to enable the 2nd menu in the info.php file of your template and assign the pages to the right menu top pages menu 2, subpages menu 1)
I am waiting for the accesrights to the WIKI, so I can updae the Tutorial by Ryan ...
cheers
Klaus