Robbie,
What you need to do is basically to use main.tpl as another html page in your site. (leaving the punbb code in, of course!)
Design a page, or use an existing page layout - nice-looking site, btw 
Paste the punbb code in the area where you want the actual forum to appear.
For example, in this page: http://homeholistics.com/new_share/forum/index.php
the forum sits in the div called c2, so the code where the div starts goes like this ......
<div id="c2">
<div id="punwrap">
<div id="pun<pun_page>" class="pun">
<div id="brdheader" class="block">
<div class="box">
<div id="brdtitle" class="inbox">
<pun_title>
<pun_desc>
</div>
<pun_navlinks>
<pun_status>
</div>
</div>
<pun_announcement>
<pun_main>
<pun_footer>
</div>
Also make sure you include all the bits that should be in the <head> for PunBB to work, then complete your page as normal. Save it as main.tpl.
Two other things that floored me for a while, which you'll need to know as I think your site is x-mapped to PHP, like mine:
[1] Add the .tpl extension into your htaccess file (so that it's mapped to PHP)
[2] If you have PHP include files in your page, you need to make special includes for PunBB. You save them into the include/user/ directory with a .php extension. In each one, put
<?php require_once('../myinclude.htm'); ?> # or whatever your include is actually called #
then change the include in your page to read
<pun_include "myuserinclude.php"> # or whatever name you gave it #
That's basically it, though I keenly feel your frustration!!! 
Now, if anybody's come up with a fab widget to make restyling the board CSS any easier, I'll be grateful to hear about it 
Cheers,
Cherry
