The owner of the site you mention actually hired me. After my initial work on the template's layout he wound up customizing it further adding some pretty cool stuff.
but in short..
Started by adding an outermost div to the top of /theme/X/header.php, and an inner div
to contain the scripts normal output, leaving room for the additional sidebars...
<div id="outer-wrapper">
<div id="header"> LOGO, etc
</div>
and at the bottom of header.php
<div style="clear: both;"></div>
<div id="main-wrapper">
Then, editing footer.php, adding this near the top ...
<div style="clear: both;"></div>
</div> <!-- eof div main-wrapper -->
<div id="sidebar">
<?
include("sidebar.inc"

;
?>
</div><!-- eof div class=sidebar> -->
and of course at the bottom of the footer.php, closing the outmost div
</div> <!-- eof div id=outer-wrapper -->
Then added something like this to the stylesheet . . . .
#outer-wrapper {width:932px;padding:0px 0px; text-align:left; float:left;}
#main-wrapper {width:510px;}
#sidebar {width:200px;margin-left:1px;margin-right:1px;}
Granted, that is an overly simplified version of what was done, because
development on that site was..., let's say, very involved.
Alot of custom work was done in the admin panel too, some of which found its way
into the current version.