It is considered important for students to participate in scientific practices to develop a deeper understanding of scientific ideas. Supporting students, however, in knowing and understanding the natural world in connection with generating and evaluating scientific evidence and explanations is not easy. In addition, writing in science can help students to understand such connections as they communicate what they know and how they know it. Although tools such as vee-maps can scaffold students' efforts to design investigations, we know less about how these tools support students in connecting scientific ideas with the evidence they are generating, how these connections develop over time, or how writing can be used to encourage such connections. In this study, we explored students' developing ability to reason scientifically by examining the relationship between students' understanding of scientific phenomena and their understanding of how to generate and evaluate evidence for their ideas in writing. Three high school classes completed three investigations. One class used vee-mapping each time, one used vee-mapping once, and one did not use vee-mapping. Students' maps and written reports were rated for understanding of relevant science procedural and conceptual ideas. Comparisons between groups and over time indicate a positive relationship between improved procedural and conceptual understanding. Findings also indicate that improved procedural understanding preceded improved conceptual understanding, and thus, multiple experiences were needed for students to connect evidence and explanation for science phenomena.