[HO455]

Many fuel cells have a internal sump area where baffles help keep the fuel pick up surrounded with fuel. As these are general used in racing applications in conjunction with rotary fuel pumps which like to have a flooded suction. Mounting rotary pumps low with the suction line in the bottom of the tank improves the reliability of the pump and improves the uninterrupted supply fuel. Your fuel cell with 2 ports was designed with this in mind. Two ports allows the use of dual fuel pumps.

If you're not planning on racing the truck then using the top suction line would be fine. If you are planning on some drag racing or autocross then using the bottom suction port would have advantages.

I would check with the manufacture of the tank to confirm that an internal sump was installed in the tank.