The Valles Marineris Explorer Cooperative Swarm navigation, Mission and Control research project aims to explore the Valles Marineris canyon system on Mars with, among others, multibody rotary-wing unmanned aerial vehicles (UAVs) comprising of a hexrotor system and a helium-filled balloon being attached to it by means of a rope. In this paper, we develop a high-fidelity closed-loop control system in MATLAB® and Simulink™ to present the application of an adequate flight controller guaranteeing (1) asymptotic tracking position control of the multibody flight system, (2) suppression of the balloon’s swinging motion in forward flight case, and (3) stabilization of the rope angle around its equilibrium for steady-state conditions. Applying feedback linearization for the outer loop and analytical backstepping for the inner loop of a nonlinear cascaded control design model of the hexrotor system, we propose an extension of the baseline flight controller by two artificial augmentation approaches to cope with the balloon dynamics. Basically, by utilizing oscillation damping feedbacks of the uncertain plant which are applied as additional commands to either the inner or the outer loop’s reference model. Simulation results are presented for an eight-shaped flight maneuver at the bottom of Valles Marineris proving that the augmentation units increase the flight controller capabilities to suppress modeling errors artificially—without changing the baseline control laws. The augmentation units actively damp the balloon motion in the forward flight case for non-steady-state conditions to counteract the rope oscillations and finally stabilize the rope angle around its equilibrium, so that the Mars vehicle is able to reach a steady-state in position when its extraterrestrial mission profile is successfully completed.