OK, I see now. Well, everything I said above is void, then. You have some major surgery to perform, in that case. I guess the first step is to dig into your WP templates and move the menu into the class="container" div. At first it will look shocking, but no matter. The styling comes later. First you need to get it into the right place.
I don't know where that code will be, but look in a few places such as header.php.
Unfortunately, the code you are working with is pretty messy, so this won't be pretty.