The web extension plugin settings are under the “SandBlast Agent Threat Extraction and Emulation” policy section in SmartEndpoint.
The setting for it is under the first action of “Protect web downloads …”.
But in the scenario you describe, I think that what you want is to exclude this internal site from inspection, as the documents there are probably trusted.
To do this, go to the 4th action. In your case it is probably “Inspect all domains and files” and add this internal domain to the exclusion list.