The newest Version of System Center Configuration Manager Current Branch (1606) is rolling out these days with a lot of new features and opportunities.
As the update is rolled out globally in the coming weeks, it will be automatically downloaded and you will be notified when it is ready to install from the “Updates and Servicing” node in your Configuration Manager console. If you can’t wait to try these new features, this PowerShell script can be used to ensure that you are in the first wave of customers getting the update.
Beginning in Configuration Manager version 1606, you can use the Configuration Manager client setting to manage the Office 365 client agent. Configure your Client Settings \ Software Updates Settings. There you can find now a new option called “Enable management of the Office 365 Client Agent“.
After you configure this setting and deploy Office 365 updates, the Configuration Manager client agent communicates with the Office 365 client agent to download Office 365 updates from a distribution point and install them. Configuration Manager takes inventory of Office 365 ProPlus Client settings.
Find more details on TechNet: https://technet.microsoft.com/en-us/library/mt741983.aspx