The Server Certificate or Import Certificate Database option is meaningful only for the package signing. In the upcoming vRealize Orchestrator (formerly known as VMware vCenter Orchestrator) Appliance 5.1, the Server Certificate is renamed as Package Signing Certificate.
If you want to set up the SSL server key-pair to vRealize Orchestrator Appliance (for Tomcat), change the dunes certificate in jssecacerts with keytool. For more information, refer to product documentation.
If you want to connect to remote SSL server (in order to trust Active Directory, import it in SSL certificates in Networking. This configures the SSL trust manager.