generally the fan or blower goes at the end of the ducting where its exhuasted out, however have also seen fans used to push air through the reflector also and in some cases it may work better that way but your would really need to try your fan in different locations to find out where it works best.
if your not using co2 wich I assume your not with a 400 you would leave one end open and the fan would cool the light and also pull fresh air into the room at the same time assuming you have an intake to pull fresh air from.