There is currently a limitation in cross-entity business process flow that prevents the stage and related records from being set pragmatically. Business process flow uses a process instance table to store the stage and the GUID's of the related records. The problem is when you are implementing process flow in an entity with many existing records. it is not practical for users to manually open each record, manually move the stage and select the record to link when there are thousands of existing records. This makes cross-entity process flow impractical for existing deployments and only really practical for people starting with an empty organization.