Service Pack 1 for BizTalk 2006 R2 is now released as beta, and includes a number of hotfixes.
(See http://support.microsoft.com/kb/974563 )
SP1 also includes a new feature, namely the ability to configure different certificates for signing outgoing AS2 messages for different parties.
Prior to SP1 for R2, we could only set one certificate for signing outgoing AS2 messages per BizTalk group.
After installation of SP1, you will see in the AS2 party properties a new tab, where you can override the group certificate.
If you do not choose to override the group certificate, the group certificate will be used by default.
We are already describing how to use this in R2 with SP1. See the topic " To configure a certificate for signing outgoing AS2 messages for a specific party" in the R2 documentation.
We are currently working on porting this feature to BizTalk 2009.