It has been recognized that design rationale is necessary for understanding and designing artifacts. In order to capture it, we focus on functional knowledge as design rationale and have developed a functional knowledge modeling tool, named SOFAST, which has been deployed in a few companies. In this paper, we aim to capture the processes related to functional knowledge which are not dealt with by the current SOFAST. We discuss a systematic description and an automatic capture system of two typical processes: modification process of functional decomposition trees in the context of designer's daily jobs, and systematization processes in which functional knowledge grows. For the implementation of the system, we extended SOFAST using an ontology-based Knowledge Management framework. Through demonstration and trial use of the system, SOFAST's users positively evaluated the system's effectiveness and expectable usefulness for their daily work.