Well yes, essentially you have 2 websites and two homepages- the first one you come to and then the x-cart one.
So there is the homepage here:
http://www.allterrainmedical.com/
and then another one here:
http://www.allterrainmedical.com/cart/home.php
So basically x-cart lives within the /cart folder.
It is rarely a good idea to have two sites like this - confusing for customers, for search engines, and as you are finding out, difficult to update and maintain.
It is not easy to get the x-cart bits (category columns etc) into the non x-cart parts of the site.
Your best bet would be to do what your designer should have done from the start, and have one, single site, based around x-cart.
If I were you, I'd start making the /home.php page look like the index page - which is perfectly possible.
Then use static pages to recreate your About Us and other such pages.
Then when you have the site built properly in x-cart - get rid of the main site and put x-cart into the root folder. It will pay dividends in the long run.