This paper presents the design methodology of a mission-oriented modular control system for marine power plants. To this end, first power profiles, power plant layouts and control systems of multiple vessels such as tugboats, offshore support vessels, cargo ships and cruise ships are analyzed. By decomposing the power profile in two components, the propulsion and auxiliary power demand, the correlation between the power profile of a vessel and its mission is derived, and an algorithm that computes the power profile using mission and vessel data is proposed. Furthermore, the correlation between the power profile and the layout of the power plant is also investigated, with emphasis on how changes in the power profile result in power plant automation modifications. A modular secondary control level is then designed to cope with the required power plant automation modifications, by combining the Equivalent Consumption Minimization Strategy (ECMS) with Supervisory Switching Control (SSC). In this paper we consider battery modifications, following the example of Wärtsilä's ZESPacks. Simulation results are used to show the performance of the proposed switching control methodology, in relation to the stability of the components in the power plant after automation modifications occur. The main contribution of this paper is the novel approach for the secondary level power plant control system, introducing modularity to the otherwise assumed fixed layout of the power plant. Furthermore, the proposed algorithm can be used to determine the expected power profile for a new mission, and to identify required modifications of the power plant equipment.