From the elements panel you can arrange your divs by dragging and bringing them on top of other divs . This might solve your problem.
The menu is not part of the animation. It's usual html and css3. When I open the submenu it goes under the animation, it covers it. And it has to be visible.
Can you just try the following :-
Open your css file in any editor and for ul element provide z-index of higher value say 1
for example :-
It worked for me , hope it works for you too.
Thank you Saurav! It helped.
I knew it will be something easy.