Complex processes require the cooperation of a variety of subsystems, such as robots, autonomous vehicles, and human-operated devices. These so-called mixed-fleet systems are found in logistics and production use cases, which also demand a high flexibility. Hence, the choreography that orchestrates the involved systems must be adaptable and reconfigurable. Enabling to add or remove subsystems flexibly during runtime requires a strong decoupling, which is found in multi-agent systems. In this paper, we explore a model-driven engineering process for service choreographies of flexible, heterogeneous, and autonomous mixed-fleet systems. Each complex process is decomposed into services and tasks, which are flexibly assigned to resources. The resulting layered service-oriented architecture is realized as an event-based system. We define requirements for modeling services, tasks, and events and evaluate different modeling language based on their applicability for each layer, i.e., BPMN, SysML/UML, and IEC 61499. We demonstrate and evaluate our architecture using a logistics use case scenario. The results show that these languages are suitable candidates for modeling event-based process models and that the diagrams can be used to capture service choreography models for decentralized systems. Future work will investigate how these models can be validated comprehensively and used for system implementation.