Yes, the thermostat will continously direct feed the Stoker motor until it heats up and satisfies the thermostat, then the PILOT/IDLE mode Timer Box (grey Box with round timer in it) will keep the coals moving and the stove going when NO heat is required by thermostat. Of course, the stove will be getting really hot and it may overshoot the temperature by a couple degrees, which is normal, since coal takes a while to heat up and cool down. I swtiched mine to a standard LUX digital thermostat with setback.
The Convection Blower will cycle on/off to circulate the heat once the stove reaches a certain temperature.
It would give better combustion if the combustion blower runs all the time, that is the way most of the newer ones operate. Just unwire it and put a plug on it and plug it in.
My Blower motor fills the opening, they may have changed it out with a slightly different one and the flange didn't line up correctly. You can put some hi-temp foil tape or hi temp silicone to fill the gap if needed.