When managing dynamic JavaScript from Java, it's essential to maintain separation of concerns and ensure that your Java backend cleanly generates the necessary JavaScript. Using frameworks that facilitate the integration of Java and JavaScript, such as JSP with scriptlets or JSTL, can be beneficial. For instance, you can create a Java class to handle the logic and then pass the data to your JSP, where it can be formatted into JavaScript. Additionally, consider using JSON to exchange data between Java and JavaScript, as it simplifies the data structure and enhances readability. Lastly, ensure that your JavaScript is modular and uses best practices to improve maintainability and performance.

Utilizing libraries like MarkerClusterer can enhance user experience, but always test the integration thoroughly to avoid performance bottlenecks, especially with large datasets like Google Maps markers.