Centrally Managed Settings

All SendTrusted settings are stored in the Windows registry.

The default settings are included in the MSI file and are stored in HKLM\SOFTWARE\DCSMailSecurityAddin. All users who run SendTrusted on the same machine will have access to those settings since the settings are stored in the HKLM (Local Machine) part of the registry. The settings architecture in SendTrusted makes it possible for different users logging on to the same machine to have different behaviors of SecureSend since settings can be controlled on a per-user basis.

Global settings

Per user settings

 Registry HKCU doc

To manage settings centrally, ADMX/ADML files that can be installed on the Domain Controller(s) but it is also possible to use GPO to directly write registry values to all clients manually. The ADMX/ADML files are typically installed on a directly similar to \\logonserver\sysvol\policies\PolicyDefinitions on the domain controller. 
By default SendTrusted reads the settings when it starts so that Outlook will need to be restarted for a change in the settings to take affect.