It shouldn't really be a problem to run fan controls in Windows. A fan profile isn't going to create instability like an overclock could. The only issue you might experience is if the software hasn't loaded your system will default to the BIOS profile. So I'd recommend setting up a rough idea of what you want in the BIOS and then use the software to make live adjustments to the fans.
To find the software you would click on See All Downloads under the Utility section and scroll for the AI Suite. Other software might do the job but that is the software ASUS provides if you want it.
A bus station is where a bus stops. A train station is where a train stops. On my desk, I have a work station…