Assessment of expertise development during training program primarily consists of evaluating interactions between task characteristics, performance, and mental load. Such a traditional assessment framework may lack consideration of individual characteristics when evaluating training on complex tasks, such as driving and piloting, where operators are typically required to execute multiple tasks simultaneously. Studies have already identified individual characteristics arising from intrinsic, context, strategy, personality, and preference as common predictors of performance and mental load. Therefore, this study aims to investigate the effect of individual difference in skill acquisition and transfer using an ecologically valid dual task, behavioral, and brain activity measures. Specifically, we implemented a search and surveillance task (scanning and identifying targets) using a high-fidelity training simulator for the unmanned aircraft sensor operator, acquired behavioral measures (scan, not scan, over scan, and adaptive target find scores) using simulator-based analysis module, and measured brain activity changes (oxyhemoglobin and deoxyhemoglobin) from the prefrontal cortex (PFC) using a portable functional near-infrared spectroscopy (fNIRS) sensor array. The experimental protocol recruited 13 novice participants and had them undergo three easy and two hard sessions to investigate skill acquisition and transfer, respectively. Our results from skill acquisition sessions indicated that performance on both tasks did not change when individual differences were not accounted for. However inclusion of individual differences indicated that some individuals improved only their scan performance (Attention-focused group), while others improved only their target find performance (Accuracy-focused group). Brain activity changes during skill acquisition sessions showed that mental load decreased in the right anterior medial PFC (RAMPFC) in both groups regardless of individual differences. However, mental load increased in the left anterior medial PFC (LAMPFC) of Attention-focused group and decreased in the Accuracy-focused group only when individual differences were included. Transfer results showed no changes in performance regardless of grouping based on individual differences; however, mental load increased in RAMPFC of Attention-focused group and left dorsolateral PFC (LDLPFC) of Accuracy-focused group. Efficiency and involvement results suggest that the Attention-focused group prioritized the scan task, while the Accuracy-focused group prioritized the target find task. In conclusion, training on multitasks results in individual differences. These differences may potentially be due to individual preference. Future studies should incorporate individual differences while assessing skill acquisition and transfer during multitask training.