In at the bottom so that the pressure fills up the majority of the cooling space inside the jacket before it exits the top hole. This will surround the motor body in a water bath increasing surface contact and the amount of time the water has to absorb heat. If you plumb it backwards, you're only washing water down across the motor body before it exits at the bottom. The closer you can get the top exit hole to be at the 12:00 position, the better... more water on the motor.
Yep, good advice there... I run a water cooled front motor plate and cool that first, then feed the lower port on the motor jacket, then out the top to the discharge hull port. The rotor runs a bit warmer and will get hot faster than the coils.
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