Matt,
Why not just surround your whole template with an IF?
Open up index.php and paste in the content of the second template index.php between the tags as shown below :<?php if (ereg( "MSIE", $ua)&& ereg( "6", $ua)) : ?>
<!-- YOUR IE6 TEMPLATE HERE -->
<?php else ?>
<!-- STANDARDS-COMPLIANT TEMPLATE HERE -->
<?php endif; ?>
You'll also have to move css and images around to bring them into the same template.
Messy and ugly. but would be interesting if it worked.