There are three ways of converting an Xml document to a flat file.
1. Flat file Assembler – this requires a flat file schema that describes the flat file format. You do not have to set the schema on the Assembler component in the pipeline. You can dynamically set the BTS.MessageType on each message, which is a reference to the schema.
2. Custom Xslt in a map. You will need to write your xslt and then implement a dynamic mapping orchestration:
http://www.biztalkgurus.com/Samples/Dynamic-Transforms-BizTalk-2006.html
3. Write a .Net component that will create the flat file for you and call this from the orchestration.