A multilayer architecture to control multirotor UAVs equipped with a servo robot arm is proposed in this paper. The main purpose is to control the aerial platform taking into account the presence of the moving manipulator. Three layers are considered in this work. First, a novel mechanism is proposed considering a moving battery to counterweight the statics of the robotic arm. Then, in order to overcome the mechanical limitations of the previous layer, the residual of the arm static effects on the UAV is computed and compensated through the given control thrust and torques. Finally, an estimator of external forces and moments acting on the aerial vehicle is considered and the estimations are fed back to the controller to compensate neglected aerodynamic effects and the arm dynamics. The performance of the proposed architecture has been experimentally evaluated.