In this paper, a control oriented nonlinear model is developed for a fuel cell based auxiliary power unit which includes a solid oxide fuel cell, an autothermal reforming, and a battery pack. Numerical steady state optimization, performed with constraints on system temperatures and fuel utilization, has been utilized to generate maps for feedforward control of the auxiliary power unit. By utilizing a virtual potential field approach, power management algorithm has been proposed for the auxiliary power unit load following while maintaining the battery's state of charge.