When you initially setup the request (CSR) for the SSL - you will enter the complete domain including the subdomain. This should issue the certificate to your subdomain.
Instructions for how to install the SSL will differ depending on type of service (web, email, ftp, etc) and the Software/Solution of that service.
Hey Did you find any help regarding installing SSl for subdomain instead of main one?
I am still having the same issue. godaddy advertise that it includes all subdomains while purchasing standard SSL and after that it's not working on any subdomain and says it's self signed.