The diverse and complex requirements of next-generation energy optimized aircraft (EOA) demand detailed transient and dynamic model-based design (MBD) to ensure the proper operation of numerous interconnected and interacting subsystems. In support of the U.S. Air Force's Integrated Vehicle Energy Technology (INVENT) program, several software tools have been developed and are in use that aid in the efficient MBD of next-generation EOA. Among these are subsystem model libraries, automated subsystem model verification test scripts, a distributed co-simulation application, and tools for system configuration, EOA mission building, data logging, plotting, post-processing, and visualization, and energy flow analysis.Herein, each of these tools is described. A detailed discussion of each tool's functionality and its benefits with respect to the goal of achieving successful integrated system simulations in support of MBD of EOA is given. Finally, some identified pitfalls in the MBD of EOA are discussed, both with respect to the described tools, and in general. Suggestions are given for mitigating the effects of, or avoiding altogether, these pitfalls.