if you want to create relationship (foreign key) between two Entities, both entities must be present in model. You can add entities from other schema to your model. For add entities you can use Object Explorer from Toad Data Modeler. It is good tool when you want to add only few tables.
After you will have Parent Entity, Child Entity and Relation in your model, you can set what you want to generate. It's more way how do it. I recommend use "Generate" checkbox that is on each form of object