Windows folder and the TrustedInstaller

By Slayer_ ·
Our application needs to add/modify files in the Windows and System32/SysWow64 folders.
But these folders are controlled by the TrustedInstaller.
OS is Win7

Taking ownership of each folder or file and setting permissions is not an option, it would have to be done remotely to 1000's of workstations. Each controlled by different crazy IT people (Or no IT at all)

I know other Applications can add files to these folders. How is it done?

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