Atomic-level visualizations serve as pivotal instructional tools in chemistry education, providing insights into the particulate level of matter, a dimension fundamental, yet typically invisible, in the study of chemistry. This research investigates how students' engagement with these visualizations influences their conceptual understanding of atomic-level phenomena. Specifically, it examines the knowledge resources used by college chemistry students (n = 15), both current and former General Chemistry students, to agree with visual representations when confronted with conflicting animations depicting atomic level acid-base neutralization reactions. Employing an epistemological framework, the study analyzed video recordings of students constructing and articulating their models and subsequently comparing these models to various animations. Through semi-structured interviews, the study probed into the students' comparison processes and their formation of statements of agreement or disagreement with specific features of the visualizations. Findings indicate that students predominantly rely on a limited range of knowledge resources when selecting their preferred animations. The study highlights the effectiveness of employing conflicting animations as a strategy to engage students in a more profound comparative analysis. An approach that leverages students' existing knowledge resources and enhances their overall conceptual understanding of the subject matter. This enhancement occurs irrespective of whether students identify the most accurate animation, suggesting that methodologies engaging students with contrasting animations can foster deeper chemistry comprehension.