Science inquiry challenges students to synthesize various ideas about complex phenomena into coherent explanations. It also challenges teachers, who must guide their diverse students' developing understanding during student-paced investigations. We describe the Idea Manager, a suite of web-based, curriculum-integrated tools that (a) guides students' knowledge integration as they generate, distinguish, and reconcile their ideas; and (b) provides means for teachers to monitor learning over the course of technology-enhanced science inquiry units. With the Idea Manager tool, students document short, text-based ideas, tag and sort them along various attributes, and exchange them with classmates. At culminating points of their investigations, students graphically organize their ideas to prepare written scientific explanations. Meanwhile, logs of idea entries, revisions, and meta-data inform teachers' and researchers' decisions about instruction and design. This paper offers an account of the design moves made in refining the Idea Manager, and highlights the importance of teacher-researcher partnerships and classroom implementations. Through designers' artifacts, classroom research findings, and teachers' and researchers' reflections, we illustrate the tool's origins; our strategies for testing new features and eliciting stakeholders' feedback, and how middle and high school classroom implementations inform the tool's continued iterations. Based on learning theory and on our own 40+ collective years of classroom teaching experience, we explain our design decisions and describe how new features and patterns for the tool's use emerged from a community of researchers. Finally, we reflect on the process of iteration that advances both theory and design, and on the value of pedagogically-driven technology design.