In this book, a high fidelity ball bearing and squeeze film damper (SFD) model including thermal effects is developed for an energy storage flywheel system with active magnetic bearings (AMBs). A high fidelity nonlinear ball bearing employs the Hertzian contact load-deflection model between ball and races, and predicts ball contact load and stress during rotor drop. Thermal growths and expansions of bearing components are estimated and applied to the ball bearing dynamics. A SFD model, based on FEM, determines oil film pressure distribution, calculates viscous damping force correcting oil film cavitation and predicts power loss due to viscous dissipation in oil film. Using the model capabilities, a variety of simulations for the energy storage flywheel system are conducted to investigate the effects of auxiliary bearing design parameters on the dynamic responses of flywheel rotor drop. Auxiliary bearing design guides to provide safe landing of rotor and to prevent high speed backward whirl are presented based on performance indices from the simulation results.