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"
Exchange 2010 and 2013:
Enable-ExchangeCertificate -Thumbprint $THUMBPRINT -Services POP, IMAP, IIS, SMTP
Note: The lack of quotation marks on Exchange 2010 on the -Services Flag!
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. Also, if you have existing services, you will need to re-list them upon entering the command.