DKX,
I've done this, and it's actually pretty simple. Take a look at my search
http://www.grand-central-chat.net/search

How I did this (with tables) is I put two new fields into site_html.pl under the global settings. (Since my site is Grand Central, I named them $gc_header and $gc_footer.

In the $gc_header, I used the qq~ print value to have the script write out the beginning variables for the table. I included the menu on the left in this, and then left the center column open. (The script will then enter each page's contents into that section.)

Then in the $gc_footer, I closed the td for the center column and made the third column, then included all of the proper table closing tags.

Then I went through all of the page subroutines and where it normally put $site_menu I changed that to $gc_header. Where it normally had $site_footer I changed it to $gc_footer.
Worked like a charm.

Hope this helps, if you need me to get more specific or post examples of code, just ask.

Raven