How to not show in top menu & only in custom menu

If those Page links are presented with template tag, wp_list_pages(), then look at using the exclude= argument.

I know this is an old post, but nevertheless my code might be useful for someone.

If you don’t want to manually add or remove page-ID’s to or from the exclude argument each time you edit your custom menu, you can add this function to your theme function.php file.
The pages which you included in your custom menu (‘name_of_your_custom_menu’) will be excluded from the default wp_page_menu.

function my_page_menu_args( $args ) {
		$array = wp_get_nav_menu_items('name_of_your_custom_menu');
		$list = array();
    		foreach($array as $key => $value) {
				$menuitem = get_object_vars($value);
				$list[] = $menuitem["object_id"];
				}
		$exclude = implode(",",$list);
	$args['exclude'] = $exclude;
	return $args;
}
add_filter( 'wp_page_menu_args', 'my_page_menu_args' );