With tasks becoming more mentally focused and operators being required to conduct multiple tasks simultaneously, it is important to not only acquire direct measurements from the brain, but also account for changes in performance and brain activity as a function of intersubject variability and task demands. Such methodology is particularly important when evaluating skill acquisition and transfer during training on a complex and ecologically valid task. To evaluate the aforementioned factors, we implemented a search and surveillance task (scanning an assigned area and identifying targets) using a high-fidelity Unmanned Aerial System operator training simulator, acquired brain activity changes via a portable functional near infrared spectroscopy (fNIRS) sensor array, and had novice participants (N = 13) undergo three sessions of easy difficulty followed by two harder difficulty sessions. Behavioral performance results indicated no significant change in scan or target find performance across easy sessions when intersubject variability was not accounted for. However, accounting for intersubject variability indicated that some individuals improved their scan performance, and they deteriorated their target find performance (Attention-focused group), while others deteriorated their scan performance, and they improved their target find performance (Accuracy-focused group). fNIRS results displayed that both groups exhibited a decrease in brain activity across easy sessions within the left dorsolateral prefrontal cortex (LDLPFC) and right anterior medial PFC (RAMPFC), while activity in left anterior medial prefrontal cortex (LAMPFC) increased in the Attention-focused group and decreased in the Accuracy-focused group. In both groups, transitioning to hard sessions resulted in a decrease in performance. The Attention-focused group displayed an increase in brain activity within LDLPFC, RAMPFC and LAMPFC, while the Accuracy-focused group displayed an increase in brain activity within LDLPFC, no change within RAMPFC and a decrease within LAMPFC. These results suggest that the Attention-focused group was able to acquire and transfer the skills needed to efficiently complete the scan task, while remaining engaged in a target find task. Alternatively, the Accuracy-focused group was engaged only on acquiring the skills needed to efficiently complete the target find task. In conclusion, these results suggest that utilizing intersubject variability as relevant information rather than noise improves assessments of skill acquisition and transfer during training on a complex task.