OK, that should enable us to help. To be sure I understand, your system has two fans in total. One is the fan supplied with and mounted on the Scythe CPU cooler system, and it is plugged into the mobo CPU_FAN header, I presume. The other is a fan supplied with your case. You say it is the "top case fan", although the Thermaltake website suggests its one fan is mounted on the back. Does not matter. You also say that the fan that shows high speed on your screen readouts is the CPU_OPT fan, so I will assume that the case fan is plugged into that mobo header.
Now, usually a case ventilation fan would be plugged into a mobo SYS_FAN header, but your mobo has enough flexibility that we can make the required adjustments without changing where you plug in your fan. Just to help you, start with your mobo manual on p. 25. You will need to get into BIOS Setup to change a couple of settings. As background, this might help. Your case fan is of the 3-pin design, and the only way to control its speed is if the mobo header it is plugged into uses Voltage Control Mode, aka DC Mode. But by default your mobo is set to use PWM mode instead. When it does things that way, a 3-pin fan can only run full speed all the time. I'll tell you how to change that.
To get into BIOS Setup to start, the manual says to push the "Del" key while it is first starting up. I find just tapping it does not work - the system often is so busy it does not notice that. Instead, push the front Power button and them immediately push and HOLD DOWN the "Del" key until the screen shows you the opening screen of BIOS Setup (p. 26). With the "MIT" heading at top selected, scroll down to the "Smart Fan 5 Settings" line and choose that. Go to manual p. 31 under Smart Fan 5 Settings. This is where you can select any of several fan headers and configure each one separately. Note under "Monitor" you select which fan - choose the CPU_OPT header, since that is where your case fan is connected. You need to set three things. Under "Fan Speed Control" set to "Normal". Under "Fan Control Use Temperature" set to use the "Motherboard" temperature sensor. Under "Fan / Pump Control Mode" set to use "DC Mode". Now escape out of this screen back to the main MIT screen (p. 26) and choose on the top the "Save and Exit" screen - see p. 42. Select the first line, "Save and Exit Setup", and hit Enter. The system will save your changes and reboot using them. That should put your top fan under automatic control based on a temperature sensor on the mobo (to sense the case internal temperature) and using the correct control method so the fan speed CAN run slower when the system is not under heavy load.