First, a general guideline: things will go much better if you use 3-pin fans on 3-pin mobo ports, and 4-pin fans on 4-pin ports.
Next, forget the PWR_FAN port on the mobo. It is designed for use with a particular set of wires coming out of SOME PSU's, and is for letting the fan inside the PSU send its speed to the mobo. This port is not intended to power case ventilation fans (although most can) and it does NOT do any control of fans.
So, first you plug your Hyper Evo that comes with a 4-pin (PWM type) fan into the mobo's CPU_FAN 4-pin port. Ignore the 3-pin version of CPU_FAN.
That gets us down to three 3-pin fans plus one 4-pin Fractal Design one for case ventilation. You say the mobo has available two 3-pin ports and one 4-pin port. If you simply don't use one of your 3-pin fans, you have one fan per port of the correct type, and there's not problem. IF you want to add the third 3-pin fan, you can do it easily. Buy a 3-pin fan Y-splitter. It allows you to connect two 3-pin fans to one 3-pin mobo fan port (and 2 fans on one port is OK, but not more). Either way, all those fans will be under automatic control by the mobo. An example of such a splitter is this:
http://www.newegg.com/Product/Product.aspx?Item=N82E16812423168&cm_re=3-pin_fan_Y-splitter-_-12-423-168-_-Product
FYI, "automatic control" of fans means this. The mobo BIOS has code in it to do this job. Although each fan port can be changed to operate in other ways, the best option most often is this automatic control, and hence it is usually the default mode set for the ports. For each port, the mobo constantly compares the TEMPERATURE as actually measured by a sensor to a target or setpoint for the device (CPU or motherboard) and adjusts the speed of the fan on that port to bring the temperature to target. As workload changes and heat generation changes, this system changes fan speeds to keep temperatures under control.
The mobo has a temperature sensor (sometimes more than one) built into it by its designers and this measurement is used to guide the CHA_FAN ports for chassis ventilation.
The CPU has its own separate temperature sensor built into it on the chip, and its signal is sent out on one CPU chip pin. The mobo uses this reading to guide the fan on the CPU_FAN port. The mobo also does a couple of other special checks on CPU measured temperature and on the speed signal from the CPU cooling fan to verify that it is working. So it really is best to use this mobo port for this fan, and NOT for any other fan.
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