Question about cpu cooler's fans

Hi guys,

Do you think that it matters where in the mobo i plug in my cooler's fans. My cooler is d14 currently one of the fans is in chasis fan 1 and the other in cpu fan 2 or something. Would it make a difference if i plug them into my fan controller?
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More about question cpu cooler fans
  1. I've connected one to CPU_fan2 and the second one into CHA_fan2. Should i connect both to cpu_fan connectors?
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