Are your fans pwm (4 pin)?
I use speedfan to control my fans, it's not the easiest to set up but it works well.
Gigabyte have there own software but I didn't like it.
I would avoid turning fans off completely. My cheap ocuk brand pwm fans are silent at there lowest speed.
With no airflow at all air within your case will get hot, a small aamoun of airflow helps a lot.