The way to get the menu into the header would be to apply it to the body, which will add something like this to the body:
<?php require_once("CSSMenuWriter/cssmw0/menu.php"); ?>
Then you would want to cut that code and put it in the head. I'm not sure why you wouldn't be able to just keep the menu at the top of the body though. That's generally how it should be designed and that is why there's a restriction on having to have the cursor in the body to apply the menu.