The ClearBlue controller should be powered up at all times and should not be connected to a timer. A microprocessor inside the controller regulates that output of minerals according to the settings for Ion Action and Large Dose. If a timer is used, these settings will not be accurate and you will have a hard time maintaining the appropriate ion level.
If you do not have a power source available that is not on a timer, you can compensate by using a higher setting for Ion Action. However, there is no guarantee that you will be able to maintain the appropriate ion level unless the controller is powered up at all time.
Note that there is no minimum flow requirement for the ClearBlue system. It is okay and preferred to keep power to the controller, even when there is no water flowing.