This paper presents a methodology to design sensor fusion parameters using real performance indicators of navigation in UAVs based on PixHawk flight controller and peripherals. This methodology and the selected performance indicators allows to find the best parameters for the fusion system of a determined configuration of sensors and a predefined real mission. The selected real platform is described with stress on available sensors and data processing software, and the experimental methodology is proposed to characterize sensor data fusion output and determine the best choice of parameters using quality measurements of tracking output with performance metrics not requiring ground truth.