Would depend on what you mean by "differentiating." While I haven't tried this with two instances on the same server, I've often created linked servers across two different servers so I can reference them with the linked server syntax. For instance - to find records in a prod table that don't exist in a dev table:
Code:
select *
from [SERVER1].[DBNAME].[SCHEMA].[OBJECTNAME] x left outer join
[SERVER2].[DBNAME].[SCHEMA].[OBJECTNAME]y on x.id=y.id
where y.id is null