Emphasis manipulation is a way to help learners by directing their attention to particular subcomponents of a learning task. This study investigated the effects of different approaches to emphasis manipulation on knowledge transfer and cognitive load. This was done by examining the impact of three task selection strategies: system-controlled, learner-controlled, and shared-controlled. Forty-five students (n = 45) in the first or second year of high school were randomly assigned to three groups and each group used a different type of task selection to manipulate emphasis in a complex learning context. The system-controlled group carried out learning tasks that were identified as essential by the system. The learner-controlled group selected and carried out learning tasks they needed to learn. The shared-controlled group chose and carried out learning tasks that they wanted to learn from a list of suggested learning tasks. The tasks had four learning phases: pre-test, training, mental-effort rating, and transfer test. After participants completed the training, their cognitive load was measured. One week after the training, a transfer test was conducted to measure the constituent skill acquisition. The findings revealed that the system-controlled task selection strategy was the most effective in optimizing cognitive load and enhancing knowledge transfer. In addition, learners benefited from personalized guidance on learning task selection based on their expertise. Given that the shared-controlled task selection method was more effective than the learner-controlled task selection, this study's results indicate that learners should be provided with information about how to select learning tasks when they are allowed to do so.