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...