A client recently asked: How do I change the default organization in a multi-entity MSCRM installation?
You can change the default organization by opening the configuration manager. In this tool you can rightclick on the organization to set as the default and click "set as default". You'll see that the name of the organization has changed to: Orgname (default).
After you perform an iisreset you need to perform some additional steps. The default organization will not change for existing users, this change will only be applied for new users created after the change.
Each user record has stored the default organization, so you would need to change them for each one of the already created users. You have two methods. Either use the tool provided by Microsoft Support or directly modify the CRM Database to change the DefaultOrganizationId in the SystemUser table.
In either case, make a backup of the databases before making any changes.