Loop and Commment Solution

I’m trying to get my comments for a post to work correctly while operating a loop within a loop.

The loop within a loops purpose is to create a main post that has a sub-journal. That sub-journal is a list of posts associated with the post. I have the loop within the loop working on posts; however, I would like for comments to be available on the main post.

The primary loop is, I belive, pretty standard code, I will include the html too:

<?php if (have_posts()) : ?>
<?php while (have_posts()) : the_post(); ?>

<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>
<p class="postmetadata"><?php the_time('m.d.y') ?> - <?php the_tags('Tags: ', ', ', '<br />'); ?> Posted in <?php the_category(', ') ?> | <?php edit_post_link('Edit', '', ' | '); ?>  <?php comments_popup_link('No Comments »', '1 Comment »', '% Comments »'); ?></p>
<div class="post_entry">
<?php the_content('read more &raquo;'); ?>
<?php wp_link_pages(); ?>
</div>

<div id="comments">
<?php comments_template(); // Get wp-comments.php template ?>
</div>
</div>

<?php endwhile; ?>
<div class="navigation">
<div class="alignleft"><?php next_posts_link('&laquo; Older Entries') ?></div>
<div class="alignright"><?php previous_posts_link('Newer Entries &raquo;') ?></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; ?>

And this is the code I post within a post through WordPress (Exec-PHP plugin activated):

<?php $my_query = new WP_Query('tag=Eng-4+Notes');
while ($my_query->have_posts()) : $my_query->the_post();
$do_not_duplicate = $post->ID; ?>
<?php the_title(); ?>: <?php the_time('m.d.y') ?>
<?php the_excerpt_reloaded(200, '<img><p>', '', TRUE, '', FALSE, 1); ?>
<?php endwhile; ?>

Now again, the main post and sub-posts generate, but the current comments for the main posts does not appear. Here is a link to the page (one single entry under Class Journal, I may be editing it too:
http://joelsimone.com/content/?p=43

So, how do I get comments working? Is it possible?

Thanks!