Depends on how it's setup, quite often if you have forced air heating the air exchanger ties into the cold air return and heating ducts of the furnace. If this is the case the furnace fan needs needs to run with the exchanger fan. I'm not sure about the AC fan, central air units have a fan on the unit placed outside and the coil is just placed in the furnace and uses the furnace fan. So which fan is on exactly?
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