Not exactly sure what you're up to, but putting in a left-hand column should just be some CSS programming.

I think a simple division in the custom.css should do. Personally, I use:
div#sideblog1 {
width: 180;
overflow: hidden;
float: left;
}

for a left-hand column. It's called "sideblog1" because I use the sideblog plugin on the left, and the sidebar on the right, with my main blog in the middle. Nice simple 3-panel approach, eh?

If you're having trouble getting it to appear in custom.css, you can add a margin to the wrapper (again, using custom.css as the example):

div#wrapper {
background: #fff url(img/bg_content.gif) repeat-y 0 0;
width: 685px;
/*width: 740px;*/
/* margin: 0 auto; */
padding: 0;
margin-left: 182px;
}

I place the div# sideblog near the top of my _main.php, which with the margin forces the sideblog into its own column starting at the top of the page (ie, the header doesn't smother the top of it).

Like this in main.php:
<div id="sideblog1">
<p><img src="randomimagecrowsnest.php" width="171" height="167" /></p>
<p>
<?php
// MostComments plugin:
$Plugins->call_by_code( 'sideblog', array(
'limit' => 5,
'blog' => 6,
) );
// Add parameters in the array.
?>
</p>
</div>

You'll recognize the standard "sideblog plugin" call there. You can easily delete that and just plop in whatever java code you want, etc...

This is all basic CSS programming stuff. Not sure if it answers your question? More advanced CSS programming materials can be found elsewhere, just do a websearch. Study up and get the look you want, eh?

Have a good one,
-MrMRA