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One can utilize relationships with multiple entity managers by setting up multiple connections to different databases, each with its own entity manager. This allows for better organization and separation of concerns within an application. For example, if an application has separate databases for customer information, financial data, and marketing data, each of these databases can be connected to a different entity manager. This makes it easier to perform operations on each specific database without affecting the others. Additionally, relationships can be established between entities across different databases by accessing their respective entity managers. This can enable powerful data modeling and analysis capabilities.