Thanks for those details. Interestingly the Bitfenix page for those fans does not specify the fan motor type, but I will assume they are 4-pin PWM type.
Your mobo has only two fan headers. One is the CPU_FAN header to be used only for the CPU cooler. The other is the SYS_FAN header at top near the rear - see mobo manual p. 12, item 4. With two case fans you need to connect them both to that SYS_FAN header. However, for what reason (we don't know yet) you believe they are connected or controlled somehow by the CPU temperature. So that raises a couple of possibilities.
1. ALL the fans may be connected to a single Splitter or Hub that is connected to the the CPU_FAN header for speed control info. If that is the case, you need to make a change. The first step would be to consider this: how to continue to control the actual CPU cooler from the CPU_FAN header. If that cooler is only ONE connection (say, a single fan), you can disconnect that from the Splitter or Hub. Then disconnect the Splitter or Hub from the CPU_FAN header and plug only the actual CPU cooler into that header. Now move the cable feeding the Splitter or Hub to the SYS_FAN header.
2. Only the CPU cooler (of whatever type) is connected the CPU_FAN header, and the two case fans are connected to the only SYS_FAN header using a Splitter or Hub. In this case you would not need to change that. But make sure that one of the case fans is plugged into the marked output for speed signals. Which is that? Depends on the design. If the device looks like a connection of cable "arms", examine each output connector for plugging in fans. Only ONE of those will have all four pins, and the others will have Pin #3 missing. The one with all 4 pins is where to ensure there is a fan plugged in. If the device is a circuit board or a box with port holes, one of those will be marked as special in some way (might even say "CPU", but do NOT use that for the CPU cooler) so plug one fan in there.
3. The two case fans are connected to your only SYS_FAN header and they are connected to each other using the "daisy chain" feature of the connector cables of those fans - no extra Splitter or Hub. No changes needed here.
After these connection changes are made, go into BIOS Setup. See your mobo manual p. 20. To enter BIOS Setup, start your computer and immediately hold down the "Del" key until the opening screen shows up (p. 21). Use F6 to get to Smart Fan 6 screen (p. 22). There choose the SYS_FAN header to work on at upper left, then go to the list at upper right. Set those as:
Fan Speed Control Normal
Use Temperature Input as Motherboard, not CPU
Fan Control Mode to PWM (for 4-pin fans), not Auto or Voltage
Fan Stop Disabled so it never stops
Fan Mode to Slope
Fan Fail Warning to Enabled so you get a warning if the fan speed signal fails
NOTE: IF your fans are of the 3-pin type - that is the MOTOR cable has three wires and its connector has only 3 holes in it - set the Fan Control mode to Voltage, not PWM. I do not expect this is the case, but just FYI.
When you get all those adjusted, use Esc to return to Main Menu, then F10 to get to the Exit Menu (p. 39) and choose Save & Exit Setup to save your settings and reboot. This should ensure that the case fans are automatically controlled according to the temperature sensor on the mobo, and not inside the CPU chip.
Note a small item. When more than one fan is connected to a mobo header (as yours will be under the daisy-chain system), the speed signal from that group that is returned to the host fan header and monitored for possible failure is ONLY from one fan. So from time to time YOU should just check that both of the fans are still working.