As a general rule, I recommend using the mobo ports for fan power, for several reasons:
(a) You get automatic control of the fan speed regulated according to actual measured temperatures in key components, so fans run what is needed, no more (less noise), and no less (more cooling when temps rise);
(b) You get mobo monitoring of fan speeds if you wish to "see" them yourself with either BIOS display or, with your mobo, an app (ASUS AI suite II, Manual p. 1-6) included on the mobo CD; and,
(c) Most mobos today (can't say for sure about yours) monitor the CPU cooler fan specifically and will give you a BIG warning or completely shut down your machine if the CPU fan fails, as a damage prevention measure.
For your specific case, I will add more comments.
1. Your mobo does not appear to have a PSU_FAN or PWR_FAN port. And I disagree a little with mace200200 - AFAIK, these ports do NO control of a PSU's fan speed, they only can MONITOR that speed if your PSU has the appropriate leads coming out of it to plug into this mobo port. The PSU does its own fan speed control internally. Since it does not ever try to control a fan speed, this mobo port can only run a case fan (if it is plugged in here instead of the special PSU leads) at full speed. But as I said, you don't have one of these, anyway.
2. I especially recommend that you connect your CPU cooler system to the mobo's CPU_FAN port. NOTE that this fan should be a 4-pin fan design. If you try to use a 3-pin fan for this job, it may not be speed-controlled, and run only at full speed always.
3. ALL four fan ports on your mobo are 4-pin. Among mobos there are several ways that 4-pin and 3-pin fans can be connected and controlled, but your mobo's manual does NOT indicate it can adapt to 3-pin fans. SO, to use your mobo's three CHA_FAN ports, you will need 4-pin fans to be sure they can be controlled properly. Now, that MAY be a problem with the three fans that come with your case. The case website does not make anything clear about the fans that are included, other than their size and speed.
Here's why Item 3 is important. Many fans supplied with a case are equipped with what are known as 4-pin Molex power supply connectors, and these are NOT the same as a "4-pin fan connector". The "4-pin Molex" (or, more correctly, the Molex 8981 connector) is about 1" wide with 4 connection wires, and was originally used for power directly from the PSU to IDE devices like HDD's and optical drives. Its 4 wires provide separate supplies of 12 VDC and 5 VDC. When used for fans, only 2 of its wires are in use - the Ground and +12VDC lines. That means the fans can only run at full speed. A "4-pin fan" connector is much smaller - about ½" wide and not as thick - and it clearly fits on a mobo fan port. A 4-pin fan also uses 4 wires, but they are VERY different from the Molex 8981 power supply system. On a 4-pin fan, the first two lines are Ground and +12VDC, again. Pin 3 is the fan speed signal. It is generated inside the fan motor as two pulses per revolution, and is sent back to the mobo port where it can be monitored for speed readout. Pin 4 in the PWM signal. There is a small chip inside the fan motor that uses this signal to control how much of the +12VDC supply actually does flow through the motor, thus controlling its speed. Older fans used 3 pins, and operate a bit differently. Pin 1 is still Ground. Pin 2 is the +VDC supply, and Pin 3 is the speed pulse signal. But in that system, the mobo achieves speed control by varying the +VDC supply from 0 to 12 VDC. (Remember that the 4-pin fan system keeps this voltage constant at 12 VDC.) But basically, a fan designed to be powered from a PSU's Molex 8981 output connector is a "2-pin fan" because it only has connections for the Ground and +12VDC lines.
Now, it IS possible to get an adapter to allow you to connect a fan designed for the Molex 8981 supply connector to a mobo fan port, BUT there are two real limits there. The obvious one is that a fan designed to be powered from a Molex 8981 connector does NOT have any speed signal to send back, and no wire for it, either. So even with an adapter to allow connection of the Ground and +12VDC lines to a mobo port, there is no fan speed readout possible. The other is that the only way to change the speed of such a fan is to reduce its supply voltage on Pin 2, just like a 3-pin fan system would. However, many 4-pin mobo fan ports do not do this - they operate ONLY in the 4-pin fan mode and keep that line at +12VDC always. So that way they cannot control the speed of that fan type.
Net result in your case is: I can't tell you right now exactly what your case fans can do, because the Cooler Master site does not say. IF they are fans with only 2 wires coming out of them and ending in the larger Molex 8981 connector, there is no real advantage to using the mobo ports for connection. You might just as well connect them directly to the PSU as they were designed. Otherwise you will have to buy real 4-pin fans that CAN use your mobo's ports properly. OTHERWISE, if the case fans actually are 4-pin fans with 4 wires from the motor ending in the smaller "4-pin fan" connector, you're all set!
Oh, one more wrinkle to note! ONE of the case fans also has blue LED lights, presumably intended for the front. I don't know exactly how those are powered. They MAY have their own power wires so that this one fan has more than 2 wires from it to its connector. OR they may be run off the main +12VDC supply, meaning that their brightness would be reduced by any system that reduces the fan's supply voltage for speed control.
The CPU Cooler fan does NOT come with your case, so you're either using one that comes with your CPU or buying one separately. I strongly recommend that you ensure it is a 4-pin fan and that you connect it to the mobo's CPU_FAN port.
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