Add custom Navigation Menu Location in Genesis.

custom_navigation.php

<?php

/*
Part One: Registering the custom Menu
*/

add_action( 'init', 'register_my_menu' );

function register_my_menu() {
	register_nav_menu( 'cpt-menu', __( 'CPT Menu' ) );
}


/*
Part Two: Place custom navigation in location of your choice
*/

/*
add the action in the location of your choice, we are implementing the menu
on before_header location, just for the sake of an example.
*/


add_action( 'genesis_before_header', 'vg_do_custom_nav' ); 

function vg_do_custom_nav() {
	?> 
	<div class="wrap nav-primary">
		<?php
		wp_nav_menu(
			array(
			'theme_location' => 'cpt-menu',
			'container_class' => 'genesis-nav-menu',
			'fallback_cb' => '',
			)
		);
		?>
	</div>
	<?php
}