SM doesn't have any special requirements for a 2012 R2 installation. Ours was only installed recently without any issues.
So, normal setup, IIS (inc port 9998 if not dedi), Firewall (open normal 110/143/587/9998 etc.), install/configure certificate, export cert and import into SM. Configure TLS ports. Bind to Mail IP. Nothing new really.
Might be worth checking or rerunning IISCrypto...remember you need to reboot the server for the full changes to take effect.
Check your SM Services too - http(s)://YourMailIP/Services or login to SM admin > Settings > Advanced Settings > Web Services