Last week I had the following problem: I published two orchestrations (with different input schemas) as WebService. The client application which of course used the same two schemas was also a BizTalk application and run in the same group. I had no influence on that and therefore the problem of duplicate schemas occured.
So I had one Receive Location for the two orchestration and needed to specify the "Document Schema" property to tell the XMLReceive pipeline which of the deployed schemas it should take. Indeed very simple but I had to search a bit: You can add two or more schema declarations in the property field seperated with the pipe(|). It worked like a charm without a problem.