Chris,
Replace the following in your theme’s index.php
<?php query_posts($query_string . '&cat=-10,-12'); ?>
<?php if (have_posts()) : ?>
<?php while (have_posts()) : the_post(); ?>
with
<?php query_posts('cat=-10,-12'); ?>
<?php if ( have_posts() ) : while ( have_posts() ) : the_post(); ?>
and you should be good.
Ross