Ok if I'm getting this right....
I copied template_default/common/tpl_main_page.php to includes/templates/my_template/common/tpl_main_page.php and inserted the analytics code into that file.
Analytics says tracking is not installed but here is the bottom of my home page source which looks ok to me (or did I mess up)?
<!--bof-ip address display -->
<!--eof-ip address display -->
<!--bof-banner #5 display -->
<!--eof-banner #5 display -->
</div>
<!--bof- parse time display -->
<!--eof- parse time display -->
<!--bof- banner #6 display -->
<!--eof- banner #6 display -->
<script type="text/javascript">
var _gaq = _gaq || [];
_gaq.push(['_setAccount', 'UA-9569526-8']);
_gaq.push(['_trackPageview']);
(function() {
var ga = document.createElement('script'); ga.type = 'text/javascript'; ga.async = true;
ga.src = ('https:' == document.location.protocol ? 'https://ssl' : 'http://www') + '.google-analytics.com/ga.js';
var s = document.getElementsByTagName('script')[0]; s.parentNode.insertBefore(ga, s);
})();
</script>
</body>
</html>