Along the bottom edge of the board in the picture (this will be the right edge of the board as it's mounted in the case) you'll see three fan headers labeled, from left to right, CHA_FAN2, CHA_FAN1, and PWR_FAN1. Although they are 2pin, 4pin and 3pin respectively, you can use any of these three, with the following notes:
CHA_FAN2 - this is your chassis fan 2 header. It's a 2pin header, so will supply the fan with 12V, but you will not get an RPM reading from it and you will not be able to adjust the speed without using a step-down adapter cable, so the fan will always run at max.
CHA_FAN1 - this is a PWM header (I believe) so you may need to adjust it's setting in the BIOS to allow for voltage control of a 3pin fan. Otherwise, you'll be able to get an RPM reading, but you won't be able to control the fan speed and it'll run at max.
PWR_FAN1 - This one runs 12V full time. You'll get an RPM reading but have the same control issue as CHA_FAN2, namely the only way to adjust the fan speed is to use a step-down adapter.
At the top of the board (right side in pic), there's a 3pin header labeled CPU_FAN2. If this is unoccupied, you can use this one, too. If I'm not mistaken, it's slaved to the CPU_FAN1 header which is where your CPU cooler fan should be plugged. Basically it will mirror whatever your CPU fan is doing on a percentage basis, e.g. if your CPU fan is running at 50% based on CPU temperature, the fan connected to CPU_FAN2 will run at 50% also.
Edit: There's an alignment key or tab on each of the headers that will match up with a groove or channel on the fan connector to make sure the right pins are being connected, so you can plug a 3pin fan lead into a 2pin or 4pin header.
Edit 2: I missed CHA_FAN3 at the upper right edge of the board as pictured. That one can be used as well.
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