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In this paper, we present a new design methodology for synchronous reactive systems, based on a clear separation between control and data flow parts. This methodology allows to facilitate the specification of different kinds of systems and to have a better readability. It also permits to separate the study of the different parts by using the most appropriate existing tools for each of them. Following this idea, we are particularly interested in the notion of running modes and in the Scade tool. Scade is a graphical development environment coupling data processing and state machines (modeled by the synchronous languages Lustre and Esterel). It can be used to specify, simulate, verify and generate C code. However, this tool does not follow any design methodology, which often makes difficult the understanding and the re-use of existing applications. We will show that it is also difficult to separate control and data flow parts using Scade. Regulation systems are better specified using mode-automata which allow adding an automaton structure to data flow specifications written in Lustre. When we observe the mode-structure of the mode-automaton, we clearly see where the modes differ and the conditions for changing modes. This makes it possible to better understand the behavior of the system. In this work, we try to combine the advantages of Scade and running modes, in order to develop a new design methodology which facilitates the study of several systems by respecting the separation between control and data flows. This schema is illustrated through the Climate case study suggested by Esterel Technologies, in order to exhibit the benefits of our approch compared to the one advocated in Scade.