If it was hooked up properly you should just leave the thermostat alone and the gas furnace won't fire till the water temperature gets below the aquastat setting.
All they should have had to do is run the W (probably white) wire from the thermostat to the common on the aquastat and the normally closed to the W on the furnace. Then the G (probably green) from the furnace to the normally open connection on the aquastat.
Oh, now that I think about it, the relay is probably to keep the fan switch working. It won't without it.
Anyway, if you have the thermostat on auto and turn it up, go check and see if the LP furnace fired. If it did something is wrong. Then turn it down and see if the fan goes off.
If you are running the fan continuous, (fan on manual) isn't your house getting too hot? The fan is all that the thermostat is controlling.