Flow-Aware Networking (FAN), after a few years of limited interest becomes again a promising concept for the Future Internet. In this paper, we present an integrated approach to ensure efficient and reliable transmission in FAN. The proposed solution is based on the central controller, which enhances an operation of particular mechanisms which compose the integrated system. The key mechanisms of the system allow to solve the problems of congestion and traffic engineering when failures occur in a network. In particular, they ensure fast acceptance of priority traffic, even in congestion, and protect such flows when a link fails in a network. Moreover, an intelligent routing algorithm for FAN allows to increase the total amount of transmitted traffic in a network. However, the mentioned mechanisms implemented alone have some drawbacks. They are eliminated in the integrated solution. The system proposed in this paper is a novel approach, which was not considered for FAN so far. We show by simulation experiments how the implementation of the analyzed solution improves transmission in Flow-Aware Networks and give some advices for operators interested in its implementation.