You should not have to alter your configure files for the download as far as where the download is stored. However... you can check both your configure files and make sure that the correct path to the files are shown... eg: here is a part of the catalog/includes/configure file.. (this is a server with Cpanel)
//the following path is a COMPLETE path to your Zen Cart files. eg: /var/www/vhost/accountname/public_html/store/
define('DIR_FS_CATALOG', '/home/YOURaccountnamehere/public_html/');
define('DIR_FS_DOWNLOAD', DIR_FS_CATALOG . 'download/');
define('DIR_FS_DOWNLOAD_PUBLIC', DIR_FS_CATALOG . 'pub/');
define('DIR_WS_UPLOADS', DIR_WS_IMAGES . 'uploads/');
define('DIR_FS_UPLOADS', DIR_FS_CATALOG . DIR_WS_UPLOADS);
define('DIR_FS_EMAIL_TEMPLATES', DIR_FS_CATALOG . 'email/');
Also check the permissions for the /download folder and make sure it is set to 755
As for the SSL - as long as you have an SSL certificate installed, you just need to change the lines in your configure.php files to true
// Use secure webserver for catalog module and/or admin areas?
define('ENABLE_SSL_CATALOG', 'true');
define('ENABLE_SSL_ADMIN', 'true');