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I was wondering what would I need to control my cpu fan and the fans in my case. And does it matter where I connect the case fans on the motherboard? 

CPU Fan is controlled by putting the cable of the stock or aftermarket cooler in the CPU slot so it is powered and controlled through the motherboard. The Case fans should be plugged in the same way but in case fan headers. You can find these in the manual of your motherboard, with more expensive and newer motherboards you are able to set your own fan speed curve depending on the temperature via the BIOS. If you want to control the case fans yourself you can either do this via the BIOS explained before or by using a fan controller which is a hub that lets you set the speed from a minimum voltage (RPM) to the max voltage (RPM).

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The different headers on the motherboard are only to help identify the fans in software. How you connect them otherwise doesn't really matter.

If you ever need help with a build, read the following before posting: http://linustechtips.com/main/topic/3061-build-plan-thread-recommendations-please-read-before-posting/
Also, make sure to quote a post or tag a member when replying or else they won't get a notification that you replied to them.

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