Q. Can I use Configuration Manager to patch Nano Server?
A. In the RTM of Windows Server 2016 it will not be able to patch or manage Nano Server using Configuration Manager as the Configuration Manager agent will not be supported on Nano Server. This will likely change for a later release. To patch Nano Server you should use Windows Update or Windows Server Update Services (WSUS). To manage the patching you can use PowerShell or Server Management Tools in Azure as shown.