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The purpose of this study was to compare flow constrained area (FCA) capacity setting methods for Collaborative Trajectory Options Program (CTOP) as they pertain to the Integrated Demand Management (IDM) concept. IDM uses flow balancing to manage air traffic across multiple FCAs with a common downstream constraint, as well as constraints at the respective FCA locations. FCA capacity rates can be set manually, but generating capacities for multiple, interdependent FCAs could potentially over-burden a user. A new enhancement to CTOP called the FCA Balance Algorithm (FBA) was developed at NASA Ames Research Center to improve the process of allocating capacity across multiple flow constrained segments in the airspace. The FBA evaluates the predicted demand and capacity across multiple FCAs and dynamically generates capacity settings for the FCAs that best meet capacity limits for all identified constraints. In a human-in-the-loop simulation study, both manual and automated capacity setting methods were evaluated in terms of their overall feasibility using measures of system performance, human performance, and qualitative feedback. Subject matter experts were asked to use three different methods to allocate capacity to three FCAs, either (1) by manually setting capacity for every 60-minute time window, (2) by manually setting capacity for every 15-minute time window, or (3) by using the FBA capability to automatically generate capacity settings. Results showed no significant differences in terms of overall system performance, indicated by similar ground delay and airport throughput numbers between methods. However, differences in individual strategies afforded by the manual methods allowed some participants to achieve system-wide delay that was much lower than the average. The FBA was the fastest method of capacity setting, and it received the lowest subjective rating scores on physical task load, mental task load, task difficulty and task complexity out of the three methods. Finally, participants explained through qualitative feedback that there were many benefits to using the FBA, such as ease of use, accuracy, and low risk of human input error. Participants did not experience the same limitations with the FBA that they did with the manual methods, such as reduced accuracy in the 60-minute manual condition, or high complexity in the 15-minute/manual condition. These results suggest that the FBA automation enhancement to CTOP maintains system performance while improving human performance. Therefore, the FBA could be introduced as a way to mitigate operator workload while planning a CTOP.