Nowadays Air Traffic Management (ATM) requires high accuracy performance to respect time constraints at specific waypoints and to sequence the traffic flow especially while climbing and landing, in order to increase reliability and safety. Current civil aviation guidance systems proposed real-time control laws to track the reference trajectories provided by the Flight Management System (FMS) while taking in consideration the overfly time constraints. With the improvement of technological devices, several types of flying vehicles are developed. They differ according to the tasks, ranges, flight conditions and performance parameters. However, these flying vehicles are nonlinear dynamic systems with variable parameters from control point of view and often under-actuated. Also, they could be requested for performing missions in unfavorable flight conditions. In this paper, an architecture to design trajectory generation and guidance functions of a Flight Management Computer (FMC) in accordance with an Embedded Flight Management System (E-FMS) requirements is defined. In order to generate a quasi-optimal trajectory as a desired reference, a composition of a path function and monotonically increasing motion function, based on B-spline functions, is proposed. A backstepping flight guidance control approach for an Unmanned Aerial Vehicle (UAV) type quadrotor is developed to achieve the generated trajectory with respect to the overfly time constrains at specific waypoints. Simulation results show the feasibility and the effectiveness of the proposed architecture.