Can you post your schema and DB version information.
Also, this screen regarding parents is confusing as it is currently implemented. You should go ahead and generate code with both Entities selected as parents since this gives you the most complete code implementation.
Generally speaking, if you choose one Entity in the relationship as a parent, the other entity should be emitted as a managed child with relationships etc.
If that did not happen, it may be due to the way the keys are being managed in the DB.
Your schema can help me to determine this.
Thanks,
jack