The feature for Free SSL allows you to generate a free ZeroSSL or Let's Encrypt SSL certificate for a DNS zone hosted at ClouDNS.
Once you have a DNS zone and the DNS zone management is delegated to us, all you have to do is to navigate to "Free SSL" button in the DNS zone management page, chose your prefered authority and click on "Activate Free SSL". After a while, your certificate will be generated and ready to be downloaded along with the Private Key.
The generated SSL is wildcard plus all hosts, for which records exist in the DNS zone (e.g. *.example.com, *.test.example.com).
Yes, you can get a free SSL certificate for a subdomain of your choice, which will not be affected by the SSL for your root domain name. To generate one, you have to add a Master DNS zone for your subdomain and make sure the DNS zone management is delegated to ClouDNS, in case the root domain is not hosted with us.