This paper proposes the design of the communications, control systems, and navigation algorithms of a multi-UAV system focused on remote sensing operations. A new controller based on a compensator and a nominal controller is designed to dynamically regulate the UAVs’ attitude. The navigation system addresses the multi-region coverage trajectory planning task using a new approach to solve the TSP-CPP problem. The navigation algorithms were tested theoretically, and the combination of the proposed navigation techniques and control strategy was simulated through the Matlab SimScape platform to optimize the controller’s parameters over several iterations. The results reveal the robustness of the controller and optimal performance of the route planner.