hi
nope, as far as i recall the install was straight forward with regard to keeping the files in the same folders as a install when one has their own certificate.
as an example the path to login for mine is showing as...
https://galaxy.xssl.net/domainname.com/login.php
galaxy being the server I'm on and domainname.com replaced with the domain being used
the login page is stored at /var/www/html
from my configuration file is the following...
define('HTTPS_SERVER', 'https://galaxy.xssl.net/domainname.com');
define('ENABLE_SSL', true); // secure webserver for checkout procedure?