AutoNav confusion

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I edited header_menu.php to add a number to each <li> ID. So my main nav looks like this:

...

<li id="nav-item-0">
<a ... >
</li>
<li id="nav-item-1">
<a ... >
</li>

...

It lets me style each menu item with CSS. My problem is on 2nd level pages the code no longer shows up. I'm guessing I put the code in the wrong place? Whats the difference between:
autonav/templates/header_menu.php
and
autonav/view.php ?


(hope that made sense!) Thanks.


complete header_menu hack is here:
http://dpaste.com/157364/

robjpc