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Use the cooling fans if you would normally use them while printing. The idea of the temperature tower is to find the best temperature to print at, and it needs to be done under your usual printing conditions.

As far as retraction with direct drive, use the lowest retraction you can get away with. This is especially true if you are using a DD with an all metal heatbreak.

Get your temperature dialed in first, and then work with retraction, starting with 0 and gradually increase by 0.5 mm. Direct drive also benefits from faster retraction speeds than Bowden setups, so try 40-50 mm/sec and increase as tolerated.