Research on note taking in pedagogical settings has received considerable attention. However, the awkwardness of integrating information across different media formats may present physical and cognitive barriers that prevent students from effectively organizing annotations from both printed and digital content while studying paper textbooks. The purpose of this paper is to develop a cross-media annotation system that incorporates a paper textbook with a computer as an integrated whole to facilitate the question-driven organization of annotations. While taking notes, students can digitally extract printed text and organize the copied passages based on guiding questions, all by using digital pens. Students can also link Internet-based learning resources to printed content to supplement their print-based studies. A user-based formative evaluation was conducted to assess the new functions of the cross-media annotation system and to explore their influence on students' note-taking behavior and performance. The results show that the new functions may facilitate the retention of key concepts of the paper textbooks and may improve knowledge construction based on explicit learning goals. (Contains 1 table and 7 figures.)