I have two website that I'm doing with similar problems. One is on the Responsive theme. The other is Attitude.
Responsive - has custom css horizontal menu that dissapears when viewing in mobile view
Attitude - has custom css verticle menu that doesn't collapse when viewing in mobile view.
I would like both to appear like the standard menu views in mobile view (3 line image with dropdown menu)
Both are clients, so any help would be greatly appreciated. I'm not experienced in responsive wordpress sites yet.