You will need to use the below command to assign/enable services to any existing certificate on the server that is correctly installed and has a matching private key.
Enable-ExchangeCertificate -Thumbprint [THUMBPRINT] -Services "POP, IMAP, IIS, SMTP"
You will need to replace [THUMBPRINT] with the certificate thumbprint this can be found by viewing the certificate under the certificate details inside the Microsoft Management Console's Certificate Snap-in for the Local Computer account described in SO14292.
Note: The thumbprint and serial number are different fields within the certificate. Also, if you have existing services, you will need to re-list them upon entering the command.