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Our .NET application needs to tweak various settings such as Microsoft Auto Updates. Example here would be "Install Updates automatically" or "Disable Automatic updates".

I know these settings can be found and modified in the registry at
HKEY_LOCAL_MACHINE\SOFTWARE\Microsoft\Windows\CurrentVersion\WindowsUpdate\Auto Update
My understanding is changing settings in the registry only, is no good in a domain environment as a GPO will potentially overwrite this setting at the next GPO update. I found this on MSDN
By default, the system processes the GPOs in the following order: local, site, domain, then organizational unit. Therefore, the computer or user receives the policy settings of the last Active Directory container processed.

Now for my question. What is the best way to permanently change these settings via our application taking Active Directory in account? Is that the purpose of the IGroupPolicyObject COM interface? The accepted answer over here http://stackoverflow.com/questions/2266797/how-to-apply-windows-group-policy-using-net gives a good example of its usuage. It looks as if he is first adding the registry key normally and then adding it again in the same manner but in the context if the GPO? What exactly does IGroupPolicyObject.Save() do?