I put a quick tutorial on which templates to edit to get your site design integrated into cubecart in this post:
How to customize cubecart templates: Before and After Example
Here's another post where I explain it:
http://www.t-shirtforums.com/p161984-post6.html
It looks like you accidentally added a {footer} type tag in your index.tpl file too many places. Or in your navigation template.
If you follow the instructions in the threads I linked to above, you'll see how to just copy the HTML from your existing design at electricthreadscorp and put that into your cubecart .tpl files.
There's only like 2 or 3 files you need to edit to start off with to get the design integrated:
index.tpl
cart.tpl
and one of the css files that has the fonts and stuff in it.