The RGB LED or fan speed settings for the CLC cooler can be changed in Flow Control and saved to the firmware of the CLC itself. Once you set the settings, you can then disconnect the USB cable if you choose without losing those settings. However, there are a few caveats:
Only static settings are able to be saved to the firmware of the CLC cooler and remain functional. Any dynamic settings, such as anything that is tied to temperature, you will need the USB cable connected. For example, changing the LED color by CPU temperature or setting a fan curve based on temperature will require the USB cable to be connected. If you have the LEDs synced with a EVGA graphics card then you do have to have the USB cable connected for the sync to work as well.