Hi Guys,
Just to clear up any confusion.
Polarity: Is the logic of the function, does the ECU activate the output to turn the device on or does the ECU activate the output to turn the device off.
Output Mode: Does the ECU provide 12v to a relay coil that is permanently connected to ground or does the ECU provide a ground to a relay coil that is permanently connected to 12v.
Clasically, thinking of a fan, a relay would be setup so that its coil is alway supplied with 12v from the car when the ignition key is on and engine running (say). To make the fan work the ECU output "activates" and connects the relay coil circuit to ground and the fan comes on, this is the way we would prefer all relays to be wired as the ECU has an easier time sinking the current through to earth rather than having to supply current out. If the fan relays coil was permanently connected to ground in the car then the only way to make the fan run is to send 12v out of the ECU when the ECU output is activated. This is the "output Mode" of the ECU output.
Let now say that the fan relay is setup so that the fan was running all the time when nothing was done to trigger the relay coil and the only way to turn the fan off was to activate the coil, this is the polarity. Normally the polarity is quite logical, if you activate the ECU output controlling the fan the fan comes on and if you were wiring a car this is the way I would assume everyone would think, however the car manufacturers often do illogical things which is why we have the option in the software.
I hope this makes it clear.