The development of software architectures that ensure both a high-level of autonomy in the mission, and the robustness to possible failures, is a challenging task. In this paper, we propose to structure the software architecture, and then its development process, around a skill management layer, based on formal skill models. This skill management layer helps to structure and test the underlying functional layer, while it provides a sound abstraction to the decision layer. This architecture has been used to support the implementation of robust behaviours, using Behaviour Trees, in autonomous UAV missions, when facing sensor failures or communication losses.