I'm pretty clued up on PHP so as soon as I sussed out what php file did what it was pretty easy to modify the php template files to do what I wanted.
The files you want live in folder of the theme that you are modifying which you will find in
There are five files of interest
header.php containing the code for (guess what!) the header
index.php which manages the fetching of the posts
sidebar.php which outputs all the stuff which usually appears in the sidebar
footer.php You've guessed it for the stuff at the bottom
style.css which is the style sheet for that particular theme
It's really a matter of adding any extra <div>'s etc that are needed, removing any output that isn't wanted and altering the stylesheet.
If you work on a renamed copy of your starting theme you can always compare to that if things go wrong.
What is the address of the website you are trying to match? I'll have a quick look at it if you like.