OK, so I have this certificate, but am confused about how to apply it to my application.
I went to the Visual Studio properties page and clicked on "signing". I checked the box that says "Sign the ClickOnce manifests" I was able to select my EV certificate from the store. All the information shows up in the "certificate box, including "Issued by: DigiCert EV code signing". I filled in the timestamp URI with the one supplied by DigiCert.
I then proceed to publish the application, but when I install it I still get "unknown publisher" and Windows 8 SmartScreen filter throws a warning.
Obviously I am either doing something wrong or there is something more I need to do, I just don't know what it is.