Connecting case fan to 3-pin CPU fan connector

I am currently using this Fatal1ty x79 motherboard:
ftp://174.142.97.10/manual/Fatal1ty%20X79%20Professional.pdf

The motherboard has three chassis fan connectors (CHA_FAN1,2,3), one 4-pin CPU fan connector (CPU_FAN1), and one 3-pin CPU fan connector (CPU_FAN2).

I connected my CPU fan to CPU_FAN1 since the connector is a 4-pin.

I have 3 chassis fans. Although all three chassis fan connectors work, I am not able to control the speed of the rear fan (CHA_FAN1) for some reason. Because of that I connected the rear fan to CPU_FAN2 instead which seemed to work. Not only that, I am able to control the fan speed on CPU_FAN2.

My question is, although everything seems to be working correctly, will it be safe for the motherboard/cpu/fans in the long run if I connect a rear chassis fan to CPU_FAN2?
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More about connecting case connector
  1. You should be fine; you can also get a case fan with built in rpm adjuster on some sizes, such as antec. You may also get this: http://www.newegg.com/Product/Product.aspx?Item=N82E16835118217 which can be installed between the fan and motherboard fan port.
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