The first steps you should take are going through all of the BizTalk Tutorials: http://msdn.microsoft.com/library/aa560270%28BTS.70%29.aspx
There are also a number of EDI Videos for BizTalk Server: http://msdn.microsoft.com/en-us/biztalk/gg153507
They cover general BizTalk Design, EDI and AS2. The EDI Tutorial will cover how Trading Partners are managed which defines how the EDI Envelope (ISA/GS) are defined.
After you're comfortable with that, you general solution will likely look something like: