I just built a system this weekend with the same case, CPU, and cooler--different mobo, though. Since this system wasn't being overclocked, I plugged all case fans and the CPU cooler fans into the mobo headers. That connector between your forefinger and middle finger disconnects, giving you the option of plugging into the board.
When you're plugged into the board, the mobo/BIOS can control the fan speed; if you use the Molex connector, the fans run at full speed all the time. On my own build, I used the Molex connectors directly off the power supply, since I was overclocking my system and I was more concerned with maximum cooling than noise--it's still super-quiet with four case fans, two CPU cooler fans, six hard drives, and an i7 930 @ 4.0GHz.
If you're not OC'ing, I'd suggest just plugging them into the mobo; less cable to deal with then, and the system will handle the fan speeds.
That is helpful. Thanks
The fan headers are identified by sysfan1 (3 pin), sys_fan2 (4 pin) , sys_fan3 (3 pin), pwr_fan (3 pin) and the CPU_fan (for the CPU cooler fans)
Not certain which fan should plug in to which header connector.
I've got a fan in the front, the rear, top and side of the case.
The CPU Fan goes into the CPU fan port. Other than that the others do not matter which port you use for which.