You can replace Neno default menu with your custom menu simply by adding a shortcode.
If you wish for example to replace the menu with an Elementor Menu you will need to grab the shortcode which is generated by the Elementor (from the Elementor Library). Open your Neno customization zone (hitting the Customize button), navigate to Header->Navigation you will find an option where you can add your shortcode. The option is named Elementor Nav menu – paste the shortcode you got from the Elementor Library in there and save.
Once you do that – the Neno menu will be replaced by the Elementor Menu. The really nice bit is that all the options of the menu will remain available to you.