Cannot seem to replace the native menu with the menu I created, so 2 menus appear

The Problem here is that you call your function inkthemes_nav() and also call the sidebar with the widget for the menu in it dynamic_sidebar('my_mega_menu').

So you have two solutions:

  • Skip the Function, just calling it from the Widget inside your sidebar
  • Skip the Sidebar, and let the Function handle the Menu

As I suppose you have to use your Menu in a Widget due to the MegaMenu Plugin (please correct me if I am wrong), I’d suggest the first Solution.

You do not have to have an extra Function for your Menu – registering and putting it into the Widget does the Trick for you.