The Smartemp 3.0 is designed to work similar to a household thermostat. The heater will try to maintain the exact temperature set on the control. Therefore, it will also cycle unless it is so cold that the heater can never fully meet demand which will cause it to run continuously in an attempt to do so.
The heater is designed to work with your vehicle battery. It should never drain your battery completely. The heater has a built in, low voltage safety. If it detects a supply voltage below 10.5v it will shut down to prevent draining the vehicle battery too much. Additionally, if it not already in operation, the heater will not start if the voltage is below the threshold.
You may need to have a load test done on your batteries to check their condition.