OK, so your mobo's manual indicates that two of the CHA_FAN headers (# 1 and 2) are 4-pin and use only PWM Mode, and CHA_FAN3 has only 3 pins but does not do any control of fans at all. That last one is only a fixed 12 VDC supply header. Thus, only CHA_FAN1 and 2 can control fans, and ONLY can do so for 4-pin fans. You have 3-pin fans, so they will always run full speed when plugged into any of those
http://www.tomshardware.com/forum/19144057/pick_as_the_solutionCHA_FAN headers.
Your only option to achieve automatic mobo control of your case fans is to use the Phanetks PWM HUb. It needs to connect to a PWM Mode header, and either the CHA_FAN1 or 2 header is suitable. It CAN power AND control the speed of your 3-pin fans. But I see from the case manual that this Hub is NOT included with your case. It is listed in the manual as an optional accessory, with instructions how to mount it. So you would need to buy this item.
If you do this, there is one part of the Hub's instructions you should NOT follow. It says you must plug the Hub's fan connector into your mobo's CPU_FAN header, and then plug the actual CPU cooler into the Hub's white Port #1. That is only because they want to be sure that the header you plug the Hub into does provide the PWM signal it needs. But your CHA_FAN1 and 2 headers DO provide that. So, plug the Hub into one of those and leave your CPU cooler plugged into the CPU_FAN header. Then connect your case fans to the Hub, making sure to connect one of them to the white Port#1. Then see your mobo manual, p. 72. It says in BIOS Setup for each of those two CHA_FAN headers you can set the Source of the Temperature reading used to control the fans on that header. You should set that to the sensor on the Motherboard, and not to the sensor built into the CPU chip. If you make that change in BIOS Setup, be sure to SAVE and EXIT.