Okay I got the sample to work. Some of the issues I ran into had nothing to do with the poor documentation. Not. Any for those of you like me that needs more spoon feeding here it goes.

Okay here is what the sample does. Simply consume a secure web service that is signed using X 509 certificate. So use the WSE 2.0 SP3 to sign your web service. Then test it with a test harness that progmatically sends the client information back to the web service. If you don't it should fail. Now go to the BizTalk side the first step is to run the Adapter Wizard for WSE 2.0 to allow for schema, port types, and the orchestration stub it creates. During the Wizard run - you will be asked to point to the wsdl of course. when you click Next, you will be presented with a dialog around authentication and certificate. Here is where I thought this UI team really need to talked to. This information screen is asking about IIS configuration information (nothing to do with the WSE 2.0 stack at all!!!!) so do not .. I repeat do not select anything here and simply click next. You then will be presented with another confusing UI screen where you will need to specify at design time which of the X509 certificates you want to use to send up to the server. And voilà .. it works .. now.. Of course complete the next steps as usual in my sample I take a sample XML and transform it to the request message needed and posts to to secure web service and get a response back and simply send it out to a file adapter port.