There is no easy to way do this, I answered this question with a code example on WPSE recently, but I cannot find it.
Basically what you have to do for sub-menu items ordering is remove them all, then add them in the order you want.
So first you have a function to remove them:
//plugin sub-menu editor as the first example
remove_submenu_page( 'plugins.php', 'plugin-editor.php' );
remove_submenu_page( 'next one' );
remove_submenu_page( 'next one' );
Then you use add_submenu_page
and add them in the order you want. http://codex.wordpress.org/Function_Reference/add_submenu_page
It seems convenluted and it is, the alternative is something wacky like this, Order Admin sub-menu items?
This is for sub-menu items, for top level items, use remove_menu_page
Edit
Index.php
is not submenu item , it is a top level item so you title is confusing!, to order top level items use this answer, https://wordpress.stackexchange.com/a/1568/1509