In apache there is an easy way you can specify different php include paths. A good way to do it is to specify it in the virtual host apache file, or in the .htaccess file. Below is an example of what you can put in the .htaccess file
php_value include_path “.:/var/www/site/include”
If you add this line to the httpd conf file you will need to restart the apache service. For any debugging see /var/log/httpd or your custom log file location.