Hi,
To answer your question, it all depends on how large your XML message is:
1) If the message is small in size, you can use XLANGs and XPath queries to modify your XML message and its contents in an Expression shape in your orchestration. Here are a couple of links talking about XLANGs and XPath:
http://geekswithblogs.net/cyoung/articles/3820.aspx
http://msdn.microsoft.com/en-us/library/ee268159(BTS.10).aspx
2) If the message is large, have a look at the following MSDN blog, to ascertain which method might best work for your scenario:
http://blogs.msdn.com/b/paolos/archive/2009/09/10/4-different-ways-to-process-an-xlangmessage-within-an-helper-component-invoked-by-an-orchestration.aspx
Hope these resources help,
Daniel.