Yes, the Mystic Light tool can control the lighting effects in those fans from the mobo's plain RGB headers, and you have connected them for that.
You will have difficulty controlling the SPEED of those fans from the case's Smart Device because it is best used with 4-pin PWM type fans. Your fans' speeds can only be controlled by changing the VOLTAGE supplied to them. They come with a connector to get power from a PSU Molex, and with Low / High speed switches. It is not clear to me if they have common female 3-pin fan connectors on them, but I suspect they do since you somehow have them plugged into the Smart Device. You could try changing that. Connect the fan's motor leads (not the RGB cables) to your mobo's SYS_FAN headers. The mobo manual says these are configured by default to use the older Voltage Control Mode (aka DC Mode). Then set each fan's individual speed switch to High so it does NOT do anything, and let the mobo headers take control of the fan speeds according to a temperature sensor built into the mobio.