To manage the complexity and the flexibility of manufacturing and shop-floor control systems is one of the major issues in today's industry. To develop flexible and easy re-configurable systems there is a need to structure the development process itself using a methodology. The objective of this paper is to present an outline for such a methodology, combining a formal modeling methodology with a project management strategy. In focus of attention is the use of a shop-floor control reference architecture and how it can support the methodology. A basic condition to succeed when using a reference architecture is the definition of the practical guidelines for how to use it. Therefore, this paper defines the activities supported by a reference architecture and gives guidelines for how and when to use it.