What is isolation relay?
Keeping this in consideration, what does a relay do in a furnace?
The electric relay in a furnace is responsible for relaying electrical power to the heating elements and the blower motor inside the furnace cabinet. The heating elements provide the heat to warm the air, and the blower motor sends this warmed air through the ductwork.
Similarly, you may ask, how does isolation relay work?
In isolated mode the relay is completely electrically isolated from the control side. Large voltage spikes, shorts, etc. will not affect your controller. Use the two center terminal labeled Positive Relay Coil Power and Negative Relay Coil Power. The next column of terminals is for the controller side of the isolation.
The most common sign of a malfunctioning limit switch is the continuous operation of your furnace's blower. Just as the limit switch won't allow the fan to turn on until the warm air has reached the right temperature, the limit switch also shuts down when the air cools to a certain temperature.