If during the activation of your website in CodeGuard you cannot see your website files like below, there is a good chance that your website files are not in your FTP/SFTP user's home directory.
As shown above, simply select the "Prefer to enter specific path?" button. This will allow you to enter the absolute path of the website on your server.
Once you've typed in the path, click "Select root directory" and continue with the website addition process.