Traditional control methods are inadequate in many deployment settings involving control of Cyber-Physical Systems (CPS). In such settings, CPS controllers must operate and respond to unpredictable interactions, conditions, or failure modes. Dealing with such unpredictability requires the use of executive and cognitive control functions that allow for planning and reasoning. Motivated by the sport of drone racing, this dissertation addresses these concerns for state-of-the-art flight control by investigating the use of deep neural networks to bring essential elements of higher-level cognition for constructing low level flight controllers. This thesis reports on the development and release of an open source, full solution stack for building neuro-flight controllers. This stack consists of the methodology for constructing a multicopter digital twin for synthesize the flight controller unique to a specific aircraft, a tuning framework for implementing training environments (GymFC), and a firmware for the world's first neural network supported flight controller (Neuroflight). GymFC's novel approach fuses together the digital twinning paradigm for flight control training to provide seamless transfer to hardware. Additionally, this thesis examines alternative reward system functions as well as changes to the software environment to bridge the gap between the simulation and real world deployment environments. Work summarized in this thesis demonstrates that reinforcement learning is able to be leveraged for training neural network controllers capable, not only of maintaining stable flight, but also precision aerobatic maneuvers in real world settings. As such, this work provides a foundation for developing the next generation of flight control systems.