Vulnerability reduction measures are taken during the early stage distributed ship system design process to ensure the availability of the required systems in a damaged state. Traditionally these vulnerability reduction measures are based on design rules or best practices resulting from past experiences. Therefore, the measures are not per definition applicable for future warships, as both the system concepts and operational environment changes. Recently developed vulnerability assessment methods are able to determine the vulnerability of a design early in the design process. With the integration of these methods in the early stage design process, the results of the analysis can be used to generate less vulnerable distributed ship system designs. This paper proposes an integral and holistic approach to optimisation of the design variables and distributed networks as these are becoming increasingly interdependent. The result of this approach is a model which generates distributed ship system designs consisting of component positions, a topology and routed connections based on a pre-defined system configuration and constraining physical architecture. Five testcases were conducted using this model, showing the necessity of the integral and holistic approach as the extent to which the contemporary design rules are implemented depends on the network complexity and operational environment.