Cayman1 hit it. To put it simpler, the controller blows air on the fuel if it decides that the pit temp needs to be hotter and stops air if it doesn't need to be hotter. It's all regulated by where you have the thermostat setting.
It works basically the same as your thermostat in your house does. You set it and it regulates the temp in the house without you having to mess with turning the furnace on and off yourself.
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