The upcoming balloon-borne imaging telescope, GigaBIT, is a three-mirror anastigmat (TMA) system with a 1.35-m primary mirror designed to perform wide-field imaging with diffraction limited resolutions in the near ultraviolet (NUV) over a 0.8-deg field of view. An in-flight alignment procedure is being developed that incorporates many techniques novel to ballooning. First, coarse rigid-body adjustments are accomplished through feedback of combined laser rangefinder and retroreflector measurements between the three mirrors. Next, rigid-body adjustments are accomplished using the field-distortion estimated misalignment of each mirror. Lastly, any residual wavefront error of the entire system is compensated by a deformable primary with a set of force actuators. As every step of the procedure will be automated, significant time reduction can be achieved from hours to mere minutes, saving precious time for scientific observations. This paper details the models and simulation results involved in the steps of the procedure.