You need to add it to your template. That way you can add the call one time, and WordPress will iterate the call so that you get it in between each of your posts.
So, for example, in the classic template it would look like this out of the box:
<?php if (have_posts()) : while (have_posts()) : the_post(); ?>
<?php the_date('','<h2>','</h2>'); ?>
<div class="post" id="post-<?php the_ID(); ?>">
<h3 class="storytitle"><a href="<?php the_permalink() ?>" rel="bookmark"><?php the_title(); ?></a></h3>
<div class="meta"><?php _e("Filed under:"); ?> <?php the_category(',') ?> — <?php the_author() ?> @ <?php the_time() ?> <?php edit_post_link(__('Edit This')); ?></div>
<div class="storycontent">
<?php the_content(__('(more...)')); ?>
</div>
<div class="feedback">
<?php wp_link_pages(); ?>
<?php comments_popup_link(__('Comments (0)'), __('Comments (1)'), __('Comments (%)')); ?>
</div>
</div>
<?php comments_template(); // Get wp-comments.php template ?>
<?php endwhile; else: ?>
<p><?php _e('Sorry, no posts matched your criteria.'); ?></p>
<?php endif; ?>
And like this if you added your calls:
<?php if (have_posts()) : while (have_posts()) : the_post(); ?>
<?php the_date('','<h2>','</h2>'); ?>
<div class="post" id="post-<?php the_ID(); ?>">
<h3 class="storytitle"><a href="<?php the_permalink() ?>" rel="bookmark"><?php the_title(); ?></a></h3>
<div class="meta"><?php _e("Filed under:"); ?> <?php the_category(',') ?> — <?php the_author() ?> @ <?php the_time() ?> <?php edit_post_link(__('Edit This')); ?></div>
<div class="storycontent">
<?php the_content(__('(more...)')); ?>
</div>
<div class="feedback">
<?php wp_link_pages(); ?>
<?php comments_popup_link(__('Comments (0)'), __('Comments (1)'), __('Comments (%)')); ?>
</div>
</div>
<?php comments_template(); // Get wp-comments.php template ?>
<!-- YOUR CUSTOM AD PER POST -->
<div class="my_ads">
<!-- do whatever you need to do to make your ad here -->
</div>
<!-- END OF YOUR ADS -->
<?php endwhile; else: ?>
<p><?php _e('Sorry, no posts matched your criteria.'); ?></p>
<?php endif; ?>
Hope that helps!
Cheers,
A