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hi i am dan i can help you with this. first how is it wired to come on now just when the furnace is runnig? what is the purpose for it being on its own thermostat?
ok so you want to make the second floor its own zone correct?
ok first just by controlling the boster fan with a thermostat will not make the second floor its own zone. the furnace will have to run too and need to isolate the first floor in order not to overheat the first floor zone. what you will have to do is install a complete zone system with a controller and dampers and make some duct modifications.
did you have any more questions about this?