Instruction in most STEM domains uses visuals to illustrate complex problems. During problem solving, students often manipulate and construct visuals. Traditionally, students draw visuals on paper and receive delayed feedback from an instructor. Educational technologies have the advantage that they can provide immediate feedback on students' visuals. This feedback allows students to learn visualization conventions and to learn new content knowledge. This paper presents a design-based research approach to develop visual tools for an educational technology for chemistry. In this research, three design tradeoffs emerged: (1) Which aspects of the drawing task should visual tools constrain? (2) How should visual tools account for variability in students' prior experiences? (3) How should the design of multiple visual tools be aligned so that students can easily transition between them? Our design-based research approach comprises three studies that address each of these design challenges in the context of chemistry visualizations. Our studies yield principles for the design of interactive visual tools for educational technologies.