Great attention is focused on the development of both remotely controlled and unmanned flying vehicles. As a matter of fact, the design of such vehicles is a topical direction of development for modern aeronautics. Among such promising flying vehicles, micro- and mini-UAVs play a leading role. The present paper proposes a method to validate the inclusion of the relevant modelling elements in a comprehensive simulation tool reproducing some of the flight phases of a mini-UAV. The energy balance budget and the dynamic response of the aircraft during the automatic flight are investigated, assessing the impact of autopilot configuration, such as altitude-airspeed holding modes and suggesting a setting guideline for flight mode selection compatible with the features of commercial autopilots.