The first fan should be an intake, pulling air in and blowing it across the radiator. The second fan should be exhaust, pulling air and heat out of the radiator. The main thing is the both go the same direction and either point out the back of the case or up (if the mounting system and your case allows it).
Generally those type of heat sinks are meant to be set up as "push-pull", one fan should be "pulling away" from the heatsink towards your rear/top exhaust, and the other fan "pushing" in the same direction as the other fan. So <---F HS <---F . F = Fan HS = Heat Sink, with them pointing towards your case exhaust.