A question was recently posted on the forums on how you can use the default pipelines in multiple applications.
I actually was stumped when I started testing the beta of BizTalk 2006 also.
The steps are pretty easy:
In your new application, right click the application and in the context menu click properties
In the properties click on references and Add BizTalk Application 1 (which is where the pipeline is installed to)
Now you can access the pipeline within your own application.