So your original question asked "...we want certain elements to be represented in the menu that's not part of the CMS site...". The instructions both Charles and I provided will do what you need.
Now on to your next issue, using a CSS List Menu with a mega menu. This can be done, you just need to know how the menu is rendered and the names of the classes that are rendered, then create your styles/classes to wrap around the ones Kentico creates.
The other and better option would be to use a Hierarchical or Universal Viewer. Do not use a repeater with any number of nested repeaters for a mega menu, you will regret it later for performance reasons.