The tuning of the navigation controllers for an Unmanned Aerial Vehicle (UAV) is a relatively long process. The reason is that the controllers can be tuned during test flights only. This tuning must be started in calm weather then continue in higher and higher wind, while the UAV reaches its given weather limits. The aim of this research is to develop a method for small-size UAVs to reduce the long time of the tuning. The verification of the hardware in the loop (HIL) simulation has a high priority. The result of this process is shown by the comparison of the test flights and the simulations. Studies have been made with various navigation methods with HIL simulation and test flights. The result of the research is a method which can be applied into reality. It supports not even the preliminary tuning but it can reveal latent defects with the simulation, so the developers can save time and money with this procedure.