The way I verify that all air is out of the system is by starting the car cold with the radiator cap off. make sure the car is on level ground. Watch the coolant level closely. as the engine gets hotter, you will see the coolant rise (and any air bubbles pop). As soon as you see the coolant about to overflow the tank, screw the cap back on.
You have just pushed all the trapped air out of the system (assuming the radiator cap is the highest point in the system, which it should be). The method works for me every time, on all my cars. Some coolant will overflow when you thread the cap in, so have a towel ready.
You said the tuner saw the fans were controlled by the ECU? he saw this on his computer? If you want to verify, you need to look at the wires coming from the electric fans. Is it connected to the main wiring harness at all?
My BMW 540i has an electric fan setup that is completely independent of the factory wiring harness/ECU, as the car came from the factory with an engine driven fan (so the ECU was never programmed to control an electric fan). My electric setup has its own wiring harness, temperature sensor, and fuse. It comes on low speed when the temp reaches 91 c, and high speed when the temp reaches 99 c. No computers.
If your fan is run independently from your ECU, then you can swap out to a different temperature sensor to a higher temp rating (like I did) to change when the fans come on.
If you fan is controlled by the ECU, then you would need to change the on/off timing of the fans within the software.
The current way the fans are operating does not dictate whether or not it is controlled by the ECU.
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