Cyber-physical systems are becoming increasingly complex. In these advanced systems, the different engineering domains involved in the design process become more and more intertwined. In these situations, a traditional (sequential) design process becomes inefficient in finding good designs options. Instead, an integrated approach is needed where parameters in both the control and embedded domain can be chosen, evaluated and optimized to have a good solution in both domains. However, in such an approach, the combined design space becomes vast. As such, methods are needed to mitigate this problem. In this paper, we show how domain knowledge can be used to guide the design-space exploration process for an advanced control system and its deployment on embedded hardware. We use domain knowledge, captured in an ontology, to reason about the relationships between parameters in the different domains. This leads to a stepwise design space-exploration process where this domain knowledge is used to quickly reduce the design space to a subset of likely good candidates. In this process, we make use of cross-domain evaluation to find feasible design options with good system-level performance.