thank you very much for using the Toradex Developer Community.
Fan direction: in my experience, I was getting better results with the fan blowing air towards the Heatsink. I would recommend any way to test your system to check if this is the case also in your application.
The temperature control is not implemented in software. Normally this software part is managed by our customers which know better the final product and its thermal design.
On the other hands, what is controlled by the module is the DVFS (Dynamic Voltage and Frequency Scaling) and Thermal Throttling.
For further information, I would recommend you to have a look at section 9.6 on page 67 of the Apalis TK1 datasheet:
I hope this helps, please don’t hesitate to use again the Developer Community if needed.