In recent years, silicon photovoltaic technologies utilizing amorphous silicon (a-Si) to form heterojunction solar cells with thin intrinsic (HIT) passivating layers have consistently demonstrated high efficiencies (>20%) including a world record efficiency of 25.6%, high fill factor's and high open circuit voltages (VOC > 700 mV). Further improvements in efficiency require a rigorous approach to better understand and improve device behavior. In this work we analyze the transport and device performance of heterojunction cells by applying a multiscale simulation methodology. Our multiscale solver consists of three primary domains, namely; the drift-diffusion (DD) domain, the ensemble Monte Carlo (EMC) and the kinetic Monte Carlo (KMC) domain. Using our multiscale methodology we investigate the role of midgap defects in the a-Si and interface defects at the crystalline silicon (c-Si) and a-Si heterointerface. Simulations indicate that recombination at the interface is a key limiting factor in device performance and contributes to the 'S' shaped current voltage characteristic. We have also used commercial device simulator SILVACO to investigate the role of surface potential at the heterointerface.