In order to understand diagrammatic reasoning with multiple diagrams, this study proposes a theoretical framework that focuses on the cognitive processes of perceptual and conceptual integration. The perceptual integration process involves establishing interdependence between relevant system elements that have been dispersed across multiple diagrams, while the conceptual integration process involves generating and refining hypotheses about a system by combining higher-level information inferred from the diagrams. This study applies a diagrammatic reasoning framework of a single diagram to assess the usability of multiple diagrams as an integral part of a system development methodology. Our experiment evaluated the effectiveness and usability of design guidelines to aid problem solving with multiple diagrams. The results of our experiment revealed that understanding a system represented by multiple diagrams involves a process of searching for related information and of developing hypotheses about the target system. The results also showed that these perceptual and conceptual integration processes were facilitated by incorporating visual cues and contextual information in the multiple diagrams as representation aids. Visual cues indicate which elements in a diagram are related to elements in other diagrams; the contextual information indicates how the individual datum in one diagram is related to the overall hypothesis about the entire system.