Generally, pci cooling fans do not generally lower overall system temperature, but can help cool specific components that do not receive much airflow.
If the pci cooler is a model that actively exhausts air from your system from the rear of the pci slot, it should be placed beneath the gpu fan.
If the pci cooler is simply a fan or a pair of fans that does not specifically vent air out the back of the computer, it should be placed above the card, on the opposite side of the gpu fan.
Either way, pci slot fans are a very poor cooling solution, and in the best case scenario you might see a five degree difference if used correctly. More often than not, they disturb airflow in the case and can even pocket warm air, and i've seen a few cases where they have increased overall system temperature.
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