Hybrid wind-photovoltaic stand-alone systems have proven to be suitable to electrify isolated communities autonomously. Moreover, the use of a combination of microgrids and individual systems has been demonstrated to be very adequate. There are a few tools to assist their design but they only consider economical and technical characteristics. However, the management of the system and the security of supply, both at a community level, are key aspects to design appropriate electrification systems for end-users, thus ensuring projects' long-term sustainability, especially in rural areas of developing countries. In this context, this paper develops a mathematical model to optimise the design of wind-photovoltaic projects combining microgrids and individual systems, and including the aforesaid key issues as constraints. Thus, the aim is to minimise the cost while meeting the technical but also the management and the security of supply constraints. Finally a validation is carried out in the real community of Alto Peru (Peru), proving that the two studied aspects allow obtaining electrification solutions with some benefits that strongly compensate the obtained slight cost increases.