Multiple Queries and Excluding Repeating Posts?

You have already figured it out but I will post an answer anyway for others.

To alter a Query, that has already been set, the easiest way is to use query_posts().

Note this will only work if run before the loop.

<?php
query_posts(array(
    'post__not_in' => array(1,2,3,4,'...')
));
?>
<?php if ( have_posts() ) : while ( have_posts() ) : the_post(); ?>
    <?php // Loop content here ?>
<?php endwhile; else: ?>
    <?php // No posts message here ?>
<?php endif; ?>