The rising popularity of commercial anatomy e-learning tools has been sustained, in part, due to increased annual enrollment and a reduction in laboratory hours across educational institutions. While e-learning tools continue to gain popularity, the research methodologies used to investigate their impact on learning remain imprecise. As new user interfaces are introduced, it is critical to understand how functionality can influence the load placed on a student's memory resources, also known as cognitive load. To study cognitive load, a dual-task paradigm wherein a learner performs two tasks simultaneously is often used, however, its application within educational research remains uncommon. Using previous paradigms as a guide, a dual-task methodology was developed to assess the cognitive load imposed by two commercial anatomical e-learning tools. Results indicate that the standard dual-task paradigm, as described in the literature, is insensitive to the cognitive load disparities across e-learning tool interfaces. Confounding variables included automation of responses, task performance tradeoff, and poor understanding of primary task cognitive load requirements, leading to unreliable quantitative results. By modifying the secondary task from a basic visual response to a more cognitively demanding task, such as a modified Stroop test, the automation of secondary task responses can be reduced. Furthermore, by recording baseline measures for the primary task as well as the secondary task, it is possible for task performance tradeoff to be detected. Lastly, it is imperative that the cognitive load of the primary task be designed such that it does not overwhelm the individual's ability to learn new material.