If you're referring to the warning that Office gives when opening a macro-enabled document, like docm or dotm, what we do is place the file in a trusted folder for the user. In our environment, that is in the user's STARTUP folder, at %APPDATA%\Roaming\Microsoft\Word\STARTUP
You can see what locations are trusted on your system by looking in your Trusted Locations. From Word, Options > Trust Center > Trust Center Settings > Trusted Locations

Does that help?