Ok you can do it this way.
function my_ajax_scripts() {
$data = array( 'ajaxurl' => admin_url('admin-ajax.php') );
wp_enqueue_script( 'ajax_url', get_stylesheet_directory_uri() . '/my-custom-ajax.js' );
wp_localize_script( 'ajax_url', 'MyAjax', $data );
wp_enqueue_script( 'ajax_url_2', get_stylesheet_directory_uri() . '/my-custom-ajax-2.js' );
wp_localize_script( 'ajax_url_2', 'MyAjax', $data );
}
add_action( 'wp_enqueue_scripts', 'my_ajax_scripts' );
You need to enqueue the scripts first and then use wp_localize_script to pass a variable to that file using the handle of that particular js file.