Assuming that you want the posts to be displayed vertically in 2 columns ( ie complete the left column, then switch to the right column), I think you many need to use more than 1 Loop:
http://codex.wordpress.org/The_Loop#Multiple_Loops
If you want the posts to display left-right-left-right, you could use a single Loop and just float the post containers using CSS.
@esmi thanks for the quick responce I have fixed this issue, but was wondering if you could help me with a related problem. On mu hopepage I have a section at the top that displayes a large feature post image, bellow this I want to list all posts again in two columns but excluding cats 16 and 17. I have been able to do this, but have been unable to get it into two columns. Can you please take a look at my code and show me how to do this as I dont want to break the code I have already writen.
<?php get_header(); ?>
<?php if (have_posts()) : ?>
<div id="content">
<!-- FEATURED CONTENT LOOP -->
<div id="feat_section">
<?php $my_query = new WP_Query('category_name=feature&posts_per_page=1');
while ($my_query->have_posts()) : $my_query->the_post();
$do_not_duplicate = $post->ID; ?>
<div class="feat_title">
<div class="post" id="post-<?php the_ID(); ?>">
<h2><a href="<?php the_permalink() ?>" rel="bookmark" title="Permanent Link to <?php the_title_attribute(); ?>"><?php the_title(); ?></a></h2>
</div>
<div class="post_author">
<p>By: <?php the_author_posts_link(); ?> | <?php the_date(); ?> | <?php the_time(); ?></p>
</div>
<div class="entry">
<?php if( get_post_meta($post->ID, "thumb", true) ): ?>
<div class="homethumb">
<img src="<?php bloginfo('template_directory'); ?>/scripts/timthumb.php?src=<?php echo get_post_meta($post->ID, "thumb", $single = true); ?>&h=350&w=624&zc=0" alt="<?php the_title(); ?>" width="624" height="350" />
</div>
<?php else: ?>
<?php endif; ?>
</div>
</div>
<?php endwhile; ?>
</div>
<!--NEWS POSTS LOOP -->
<div id="news_section">
<?php
if (is_home()) {
query_posts("cat=-16,-17,");
}
?>
<?php if (have_posts()) : while (have_posts()) : the_post();
if( $post->ID == $do_not_duplicate ) continue; update_post_caches($posts); ?>
<div class="post" id="post-<?php the_ID(); ?>">
<h2><a href="<?php the_permalink() ?>" rel="bookmark" title="Permanent Link to <?php the_title_attribute(); ?>"><?php the_title(); ?></a></h2>
<small><?php the_time('F jS, Y') ?> <!-- by <?php the_author() ?> --></small>
<div class="entry">
<?php the_excerpt(); ?>
</div>
</div>
<?php endwhile; endif; ?>
</div>
<div class="navigation">
<div class="alignleft"><?php next_posts_link('« Older Entries') ?></div>
<div class="alignright"><?php previous_posts_link('Newer Entries »') ?></div>
</div>
<?php else : ?>
<h2 class="center">Not Found</h2>
<p class="center">Sorry, but you are looking for something that isn't here.</p>
<?php include (TEMPLATEPATH . "/searchform.php"); ?>
<?php endif; ?>
</div>
<?php get_sidebar(); ?>
<?php get_footer(); ?>
