This paper discusses the construction and testing of hardware-in-the-loop simulations using a commercial software simulation package and a custom-designed simulation. It discusses the process of integrating an avionics computer with Unmanned Aerial Vehicle (UAV) sensors and actuators, designing and implementing linear and non-linear simulations of the aircraft, setting up the control system architecture and evaluating various control laws through the hardware-in-the-loop simulations. Extensive comparisons are made between the different versions of the simulations to ensure that every step in the piecewise development of the final simulation is correct. Several types of control systems were tested on this final simulation. However, despite their adequate tracking of reference trajectories, none are robust and mature enough to yet consider for in-flight testing. A future work section discusses options for further development of the control system and modifications to the simulations to increase their fidelity. A straightforward, detailed and logical process is provided for setting up hardware-in-the-loop simulations of small UAV systems similar to the one described here, and evaluating control system performance. Important time and cost savings from lessons learned in this process are also provided.