When you add a web reference to a service, a “web port” is created that contains all the operations of the designated service. So when you create a new “configured port” in your orchestration, you reuse the auto-generated port, and all your operations are available. Then, it’s up to you as to which operations you wish to call.
There are a number of resources online and in MSDN about using BizTalk and web services together (http://msdn2.microsoft.com/en-us/library/ms935219.aspx).