Most unmanned aircraft systems (UAS) are, at present, designed for military purposes and very few civil applications have been developed mainly because the lack of a regulation basis concerning their certification, airworthiness and operations. UAS operations have always been solutions highly dependent on the mission to be accomplished and on the scenario of flight. The generalized development of UAS applications is still limited by the absence of systems that support the development of the actual operations. Most current UAS solutions, if not remotely piloted, rely on waypoint based flight control system for their navigation and are unable to coordinate the aircraft flight with payload and mission operation. In this paper, an architecture for providing automation in UAS application is presented. This architecture is part of a UAS-specific distributed service-oriented architecture designed to enable easy reconfiguration and deployment of UAS in a wide range of scenarios without (or very little) additional system development. Flight, payload and mission service coordination, service interfaces and message interactions between services are discussed in this paper. Finally, a preliminary prototype of these services has been implemented to validate the purpose architecture specification. Additionally, a helicopter-based UAS is being developed to test in real scenarios the automation capabilities provided by the USAL architecture.