Researchers from the NASAAmes Flight Cognition Laband the FAA’s Aerospace Human Factors Research Lab at the Civil Aerospace Medical Instituteexamined task and workload management by single pilots in very light jets, also called entry-level jets.This exploratory simulation study was also performed to generate baseline data to be used in future NextGen-oriented studies and was conducted in a Level 5 Cessna Citation Mustang flight training device (for simplicity, referred to as a “simulator” throughout the rest of this document).In addition to the use of the simulator, data collection included voice analysis, instantaneous self-assessment of perceived workload, NASA Task Load Index workload measures, researcher observations, final debriefing interviews, Cockpit Set-up Preferences questionnaires, Demographics questionnaires, and Automation Experiences and Perceptions questionnaires. Within the current paper, we describe the process by which we designed our human-in-the-loop (HITL) simulation study and the methodology used to collect and analyze the results.For a summary of the results, please refer to Burian, Pruchnicki, Rogers, et al. (2013). The purpose of this document is to describe much of the work required in the development of HITL simulation study materials, the design of experimental scenarios, and the management and transformation of data required in preparation for analysis.