Fractal Design and mobo Power fan header?

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This maybe a silly question, my motherboard has a power fan header on it and the fan at the front of the FD R3s connector only fits in this header, is this correct?

I'd have thought it should be wired to Sys Fan 2 but it doesn't fit.
 
I probably didn't explain myself too well here, I've got two sys_fan headers and 1 pwr_fan header (not CPU fan) and I don't know what the difference is, does anyone know? It's a gigabyte GA-Z68A-D3-B3 motherboard.

Currently my rear fan is plugged into SYS_FAN1 and my front fan is plugged into PWR_FAN even though there is a SYS_FAN2 a little further away, It just seems a bit noisy TBH.
 
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