Hi,
You are dealing with two separate topics here:
1) Electronic Data Interchange (EDI): it’s a pretty complex subject in itself and I STRONGLY suggest that you educate yourself on this before trying any implementation so that you know what you are getting yourself into. Here’s a book that I would recommend “Pro EDI in BizTalk Server 2006 R2” by Mark Beckner and you can find more information at this link:
http://www.springerlink.com/content/r534j09111836r44/
2) Exposing BizTalk schemas/orchestrations as a SOAP web service or WCF service: since you are using BizTalk 2006 R2, I STRONGLY recommend that you expose any schema/orchestration as a WCF service for forward compatibility and interoperability. You can read up more information on the process of publishing WCF services at this MSDN link:
http://msdn.microsoft.com/en-us/library/bb226350(BTS.20).aspx
I hope this is enough information to get you started and on your way to developing BizTalk solutions with EDI.
Happy Holidays,
Daniel.