Check Section 4.6 of your manual on p. 97 - that's where you can adjust fan settings. Your mobo has 3 chassis fan ports - one 4-pin at the bottom edge, and two 3-pin in the middle of the board. Your case came with 3-pin fans.
You should be aware that a 3-pin fan plugged into a normal 4-pin fan port will always run at full speed. SOME mobos allow you to alter the way that 4-pin port operates to make it behave like a 3-pin fan port, but I don't know whether yours does or not. So check the BIOS settings in Section 4.6 to see if you have that option for the CHA_FAN_1 port.
Alternatively, you could simply connect both of your fans to the CHA_FAN_2 and _3 ports, then configure each under Section 4.6.
The manual does not make it clear what options you have for adjustment. Usually you can disable a port (some of these may be by default), set it to automatic control, set it to a fixed speed, or set it to a version of automatic control in which you custom specify what speed it will run for certain temperature values. For the case fan ports, the "temperature" it uses is sensed by a probe built into the mobo itself.
(For the CPU cooling system, the temp used is from a sensor built into the CPU chip.)