I will assume you are using postfix as your smtp sever.
Postfix right now doesn't supports multiple certs for multiple domains so you can only use one certificate for all your domains/subdomains.
The solution to this postfix limitation is using a SAN certificate, a SAN certificate allows you to authorize several domains and subdomains on a single cert.
I'm having some trouble deploying mine but here is a post with my main problem and some information that may be valuable to you 