The Mega Menu (the navigation created in the Menu Builder) uses the same Menu Color and Menu Color - Contrast Color settings shown in Theme > General. You can change them from either place: editing the two colour rows in Theme > General, or opening Menu Builder (admin/menubuilder) and using its Background color / Text color pickers at the top of the page — both write to the same underlying colour settings, so a change in one place shows up in the other. There is no separate colour setting just for the Mega Menu.