How To: Configure WMREST for Windows authentication
Instructions provided describe the steps to configure the WMREST Web site to use Windows authentication integrated with IIS security. This only applies to systems in which Workflow Manager Server is installed on top of ArcGIS Server .NET.
As part of Service Pack 3, Esri included a web-secure.config file that has the security settings under the wmrest Web site folder.
In ArcGIS Manager, modify the security settings to use Windows authentication.