Recent emphasis on optimization of engine technologies with ancillary subsystems such as power and thermal management has created a need for integrated system modeling. These systems are coupled such that federated design methods may not lead to the most synergetic solution. Obtaining an optimal design is often contingent on developing an integrated model. Integrated models, however, can involve combining complex simulation platforms into a single system of systems, which can present many challenges. Model organization and configuration control become increasingly important when orchestrating various models into a single simulation. Additionally, it is important to understand such details as the interface between models and signal routing to ensure the integrated behavior is not contaminated or biased. This paper will present some key learnings for model integration to help alleviate some of the challenges with system-based modeling.