OP, in your second post your problem is quite clear, but I don't think you understand all the issues. You say, "the controller has an auto feature based on heat", but what heat?
Most mobos have TWO automatic fan control systems. Each is based on a temperature sensor to measure the actual temps at particular spots, and vary cooling according to that. These are simple feedback control loops - each uses changes in fan speeds to keep a measured temperature within range of a setpoint. The real key in each case is what temperature is being measured and used?
The CPU_FAN port runs the CPU cooling fan. Its associated temperature sensor is actually built into your CPU itself, so it is measuring the actual temp inside your CPU chip at some critical spot. NO third-party fan controller can get at that signal and use it, so you actually can NOT control any fan according to that sensor. You MUST let the mobo's system do that job IF you want to control that way. If you do not, you can only control the CPU fan's speed with some less-pertinent method - either a temperature measured by some other sensor mounted (where?), or just manually set your fan speed as you like. But some simple inside-case temp is not a good measure of the temp inside your CPU.
Now, the mobo has at least one separate sensor mounted somewhere in the mobo itself, and that is the one it uses for controlling case fan speeds. If you prefer to use a third-party controller with its own temp sensors you mount somewhere in the case, I can believe you might pick a sensor signal that is just as valid as the one the mobo would use. So that make sense to me, but the CPU cooling control is better left to the mobo CPU_FAN port, I think.
If you cannot find a place in you BIOS to tell it to ignore the CASE fan speed signals when you use your third-party fan controller, maybe the way is to tell the BIOS to Disable the case fan automatic control system entirely.