Cyber-Physical Systems in general, and Intelligent Transport Systems (ITS) in particular use heterogeneous data sources combined with problem solving expertise in order to make critical decisions that may lead to some form of actions e.g., driver notifications, change of traffic light signals and braking to prevent an accident. Currently, a major part of the decision process is done by human domain experts, which is time-consuming, tedious and error-prone. Additionally, due to the intrinsic nature of knowledge possession this decision process cannot be easily replicated or reused. Therefore, there is a need for automating the reasoning processes by providing computational systems a formal representation of the domain knowledge and a set of methods to process that knowledge. In this paper, we propose a knowledge model that can be used to express both declarative knowledge about the systems' components, their relations and their current state, as well as procedural knowledge representing possible system behavior. In addition, we introduce a framework for knowledge management and automated reasoning (KMARF). The idea behind KMARF is to automatically select an appropriate problem solver based on formalized reasoning expertise in the knowledge base, and convert a problem definition to the corresponding format. This approach automates reasoning, thus reducing operational costs, and enables reusability of knowledge and methods across different domains. We illustrate the approach on a transportation planning use case.