System Center 2012 R2 Configuration Manager is the fifth component to be upgraded. If applicable, install Service Management Automation, upgrade Orchestrator, upgrade Service Manager, upgrade Data Protection Manager, and then upgrade Operations Manager before you upgrade Configuration Manager.
Configuration Manager Upgrade Sequence
Put all Configuration Manager servers into an Operations Manager maintenance mode.
On the computer hosting the Orchestrator Deployment Manager, uninstall the IP for Configuration Manager.
Upgrade Configuration Manager using the procedures outlined in the Upgrade Guide for Configuration Manager.
Post–Configuration Manager Upgrade
Take the Configuration Manager servers out of maintenance mode.
Register the System Center 2012 – Configuration Manager R2 integration packs on System Center 2012 - Orchestrator R2.
Make sure that the following connections with Configuration Manager continue to function:
Configuration Manager management agents
System Center 2012 Endpoint Protection agents on the component servers
Make sure that the two Service Manager connectors continue to function.
Make sure that the IP continues to function with Orchestrator.
Make sure that the Operations Manager management pack continues to function: