The pump should draw from the bottom of the (front) heat exchanger, from there to the rear inlet of the intercooler (coolest water closest to throttle body), from the intercooler back to the top of the heat exchanger. (which, incidentally is how your engine coolant is run, pretty much)
If you have the factory lines, they all line up and fit only one way, but might be slightly different than my description above due to packaging reasons.
-Charlie