With BizTalk Server 2009 it is possible to debug a BizTalk map within Visual Studio. This is very cool. But, at the moment not all mappings are supported. When you use functoids which references an external assembly then you can’t debug.
So, how does this work? Consider the next mapping:
Next, right click on the map and click debug:
Some messages appear. Just click yes, or overwrite or whatever appears 
Finally next screen is shown:
Press F11. On the right screen you can see the generated input file:
You can also debug the functoids:
And see the value of the properties:
In the right pane you can see how the Xsl is building your output Xml:
Another screen example:
As you can see, Microsoft did a good job. When you have large mappings with multiple pages with functoids, lines, xslt etc this can be very handy.
