About the mega menu category, in this case, you can’t add submenu item into a menu item that set as mega menu category. Please try to remove the submenu item from the menu item that set as mega menu category. Let me know if you need some help in there to setup it.
I’m not quite sure with what kind of multi-level menu that you mean on this thing. Anyway, can you please provide me an example of the menu that you want to have? Maybe i can provide you some solution to achieve your need.