Just be sure if you're putting the motherboard heatsink back above your drive, to remove the protective plastic sheet over the thermal pad (just like on the CPU cooler), which should be on the inside surface of the heatsink.
Once your drive is installed and secured by a screw or tab, put the heatsink back where it was on top of your drive, unless your drive has a heatsink of its own. Just be sure if you're putting the motherboard heatsink back above your drive, to remove the protective plastic sheet over the thermal pad (just like on the CPU cooler), which should be on the inside surface of the heatsink.