I was having that exact problem, needing parent categories to be in the header. I believe it is actually determined in the /classes/categories_ul_generator.php as to how it calls for things, but I am not PHP savvy.
Turns out there's another version of this mod that does JUST that.
HERE
NOW my issue is I need two categories to go straight to listing All Products in that category while one category would stay the norm, so if anyone can help with that it'd be appreciated.