The CPU cooler will plug into your mobo whereas your case fans will run of your psu. There is no control for the case fans as far as I know. I have one on mine and it just runs a constant 1200rpm and doesn't really do much. It is a blue LED fan and just makes my case look nice tbh
In terms of cooling case fans help TO A POINT. It is very rare that your components will become too hot unless your overclocking your cpu and gpu extensivley
and I mean to seriously highspeeds.