Crystal Pure Connection to IntelliPro pump

I purchased a Crystal Pure Salt System.  I have a variable speed Intellipro VSF pump.  The pump is wired to a Timer clock/box, but done so that it is always powered on.  (I assume if the timer were to power it off at this location, the memory in the pump would be wiped.)  The pump turns on and off via its own program schedules.   My question is how do I connect the Crystal Pure since it is not supposed to be powered on continuously if I do it per the Timer option in the manual.