It doesn't matter which port you use. It is a side-by-side two pass arrangement so it doesn't matter. If it were arranged where both passes are subjected to the full face of air flow, i.e. front/back, then it is VERY important which is the "in" or "out". In that arrangment you always want the hottest fluid seeing the hottest air. In other words the port serving the back side of the cooler would be the "in" and the front port would be the "out".
A lot said about something that doesn't apply to you but I'm in a sharing mood and it distracts me from doing what I'm supposed to be doing.
Since I'm rambling here is some more worthless information.
I converted mine to a singel pass like the original cars to reduce pressure drop. This can be accomplished by welding a #12 male bung on the top plenum of hte cooler. You will need to machine the base plenum to remove the divider if you choose to go with a single pass. The prefered "in" port on a single pass cooler would be one of the bottom ports. If you are using a wet sump motor the extra fitting on the base of the cooler would make a great connection point for an "accusump".
Attached is a picture of what I ended up with.
Cooling on a single pass arrangement is basically the same but much less pressure drop as compared to a two pass. Oviously the two pass works.
Now that I'm on a roll here is some more information. Unless you properly position the cooling relative to the inlet duct and provide a fairly positive seal between the duct and the cooler then the cooler really doesn't do that good of a job. This is easy to se by simply reaching through the cooling duct and feeling the relationship between the duct and the cooler. These coolers are actually the same coolers used on large displacement piston aircraft motors and have a sizeable pressure drop on the air side.
If you decide to do it right and provide a positive seal for the air then you will likely experience a "danged if I do and danged if I don't" situation. You will likely have too much cooling of the oil except under extreme driving condtions which means you would need to consider using an oil temperature thermostat to maintain proper oil temperatures.
All that said, if you are driving the car on the street just hook up the cooler in the two pass arrangement and let the air bypass it and all will likely be good.