The integration between Microsoft System Center products is always one of the marketing promises. A lot has been done in that direction within the last years. One topic is still not working as expected, which is related to the interopability between SCCM and SCOM.
Short explanation: If you install software or software updates through Configuration Manager you normally want to disable the monitoring (alert creation) in Operations Manager. The problem is, that it looks like the function is implemented, but it is not fully implemented. See System Center 2012 Operations Manager Unleashed.
Here are the details.
You can set the option to “Disable Operations Manager alerts…” for applications, package or software updates. Here are the screenshots for it:
Application: 
Package (only 2012 SP1): 
Software Update: 
The question is, what is happening in the background when you select this option?
The real thing, which happens, is that the System Center Management Service gets paused.
This was already the case in ConfigMgr 2007 with SCOM 2007 R2. See.
What is the effect in SCOM?
The Health Service object gets unavailable, but the Health Service Watcher stays active.
We will not see the alert “Health Service Heartbeat Failure” because the monitor is in a warning state and it only creates an alert when it is in a critical state.
Do we have a problem with that?
Yes. The system is not really in maintenance mode. If the system needs to reboot after the installation minimum one alert will be created: Failed to Connect to Computer. See these posts:
https://support.microsoft.com/en-us/kb/942866
http://thoughtsonopsmgr.blogspot.de/2009/04/maintenance-mode.html (this one is for SCOM 2007 R2, but it is still current.)
Also if you implemented my solution for greyed out agents, then you will get an alert listed with these servers which get the System Center Management service paused, because they are greyed out and no Health Service Heartbeat Failure alert is created!
You can use other options to set the maintenance mode in SCOM for installing software or implement software updates until a better integration for setting this functionality is implemented into SCCM 2012 directly:
- With System Center Orchestrator 2012
- Use a task sequence and run a PowerShell script to start and stop SCOM Maintenance Mode.
SystemCenterTipps 