Implementing a control law on an Unmanned Aerial Vehicle can be problematic when the existing autopilot system is incompatible with the controller structure. This paper extends the control strategy that incorporates a pre-existing autopilot system in a closed-loop control law design [1]. In [1], the control scheme explicitly involves the autopilot in the controller derivation, based on an assumption that the autopilot is able to follow the input commands in an exponential manner, which may not be possible. In this paper, we present a novel controller design that incorporates unknown autopilot gains. The controller is proved to guarantee that the tracking error converges to an ultimate bound, which is a function of the maximum magnitude of unmeasured disturbances and control gains. Simulation results are used to demonstrate the effectiveness of the proposed controller.