How to integrate wordpress with existing site properly

Hi guys, I have my own website and I have installed wordpress 3.0 in the /blog/ directory of the website.

To have wordpress match my theme, I copied the twentyten theme and renamed it mytheme, then copied my sites index.php over /blog/wp-content/themes/mytheme/index.php, and added the following code:

above my <body> tag I put:

<?php get_header(); ?>

in my main content div I put:

<div id="container">
<div id="content" role="main>
/* Run the loop to output the posts.
* If you want to overload this in a child theme then include a file
* called loop-index.php and that will be used instead.
get_template_part('loop, 'index');
</div><!-- #content -->
</div><!-- #container -->

and after my main content div I put:

<?php get_footer(); ?>

Now, this works PERFECTLY. My blog posts show up in the right place and that is ALL that shows up (it’s all I want) - and it looks like the rest of my website!

However, when I click on comments it is a mess and doesn’t match my sites design. I tried pasting the code from comments.php into a new comments.php that had my site layout in it, and this ‘almost’ works: The post replies are shown in my main content div, along with the post-a-comment-form. However, the main blog post is showing at the top of the page outside of my divs, and the sidebar is showing at the bottom of the page outside of my divs.

I want the main blog post to show up in the main div as well, and I don’t want the sidebar at all. Works fine for the main blog page.

Any help would be appreciated beyond anything I can say - this is the last thing I have to figure out to finalize my families website and I’ve been hurting my head trying to make it work.

Here are some example screenshots of what I am talking about:

the index working correctly:

the top of the comments page, not working correctly:

the bottom of the comments page, not working correctly:

I am really desperate and have tried to read about this but can’t find or understand how to do it properly.