Here's a tutorial to move your site to root and maintain search engine rankings:
Move X-Cart To Root.
If you don't move your site to root, then at least set a home.php directory index in your subfolder .htaccess file do a 301 redirect from root to your subfolder by putting an index.php file in root with the following content (replace /shop/ with your folder):
Code:
<?php
header('Location: /shop/',TRUE,301);
?>
Our CDSEO program includes a home.php directory index and to consolidate pages it also does a 301 redirect to / when
http://www.example.com/home.php is accessed directly.
If you are running Zeus then you can set your directory index in your control panel.