code in functions.php

<?php

// de-queue navigation js
add_action('wp_print_scripts','tto_dequeue_navigation');
	function tto_dequeue_navigation() {
		wp_dequeue_script( 'twentytwelve-navigation' );
}
// load the new navigation js
	function tto_custom_scripts()
{

// Register the new navigation script
	wp_register_script( 'primarymobile-script', get_stylesheet_directory_uri() . '/js/navigation.js', array(), '1.0', true );

// Enqueue the new navigation script
	wp_enqueue_script( 'primarymobile-script' );
}
add_action( 'wp_enqueue_scripts', 'tto_custom_scripts' );

// Add the new menu
register_nav_menus( array(
	'primary' => __( 'Top Menu (Above Header)', 'tto' ),
	'secondary' => __( 'Primary Mobile (Below Header))', 'tto'),
) );

?>