The performance of double-layer microchannel heat sinks are evaluated comparatively for the parallel flow, counter flow, and transverse flow configurations with and without hotspots as heating condition. Conjugate heat transfer analysis is performed by solving three-dimensional Navier-Stokes and energy equations using a finite volume solver. The flow is considered to be steady, incompressible, and laminar. Functional relations between the thermophysical properties of water and temperature are developed and used for numerical calculations with variable fluid properties. The thermal resistances, maximum temperature increase at the hotspots, temperature variation among the hotspots, and pressure drops are evaluated for the three heat-sink designs with two hotspot schemes (single hotspot at the center of the heat sink and multiple hotspots distributed uniformly at six peripheral locations). For the single-hotspot case, the parallel flow heat sink exhibited the lowest thermal resistance and temperature rise at the hotspot. For all the six multiple hotspot cases, the transverse flow heat sink exhibited the lowest thermal resistance and temperature variation among the hotspots.