Fuel Cells provide an attractive alternative to battery powered Unmanned Aircraft Systems (UAS) as they maintain the simplicity of an all-electric vehicle architecture while taking advantage of highly energy-dense fuels. Unfortunately, the overall energy and power density of the power and energy (P&E) system cannot be determined from the fuel and fuel cell technology without also including the context of the associated aircraft and mission. These outside requirements play a particularly important role in the design of Small UAS (SUAS) P&E systems where the fixed weight of the fuel cell plant may approach or exceed the weight of the fuel utilized. Over the past seven years Protonex has developed fuel cell power systems for a number of different SUAS, creating an empirical database and methodology suitable for future SUAS design efforts.This methodology centers on estimating the weight fractions of the power conversion and energy storage systems in comparison to the overall vehicle weight. The author's previous work focused on presenting this methodology on a macro scale for the initial phases of a conceptual design. As the UAS design concept matures additional dependencies emerge, particularly due to the impact of mission requirements such as the required environmental operating envelope.In this paper the authors expand the design methodology to include the impact of aircraft level requirements and design decisions. The expanded methodology is presented conceptually and in practice via application to specific UAS design examples.