We're trying to rethink how we handle these unique sections. In our current setup, we do all of the cross-listed/merged sections on the registrar's side, and then the newly-combined course is pushed to Blackboard like any other. This has a few disadvantages, most significantly, merging or un-merging courses mid-semester isn't an option since it would mean the students' work thus far couldn't be transferred to the new course(s). Using Blackboard's parent-child functionality wouldn't help.
At the moment, I push the registrar's office to handle all of that before the semester begins, but they don't like being locked in. How does your institution handle it?