This paper proposes a new and powerful methodology to the evaluation of guidance, navigation and control algorithms (GNC) in Software-in-the-Loop (SiL) flight simulation using Microsoft Flight Simulator (MSFS). The SiL was assisted by the Flight Variables Management System (FVMS), a Graphic User Interface (GUI) that fully interfaces communication between MSFS and general purpose custom GNC algorithms. The originality of this new approach is to make the FVMS communication layer completely transparent to the designer so that full attention may be focused exclusively on guidance algorithm development and the debugging process as well. Furthermore, the application may be extended to both multi-engine fixed and rotary wing aircraft. When it comes to the design, development and validation of brand new control algorithms of GNC for unmanned systems, SiL flight simulation becomes an exceedingly useful tool since end-product may misbehave in-flight. It impacts over avoiding hazard situation of crew and population in the ground and on preserving expensive equipment of being damaged. To illustrate FVMS capabilities and assets on GNC systems design, a nonlinear path following algorithm is set up. FVMS GNC module is endowed with a full map interface and a mission management through which one may build/rebuild the UAV path on-line. The results demonstrate the potential of the framework on the implementation of either simple or more complex solutions for the GNC problem.