Can any case fan be controlled by M/B header?

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.

Thanks for the reply. I'm not overclocking. My office at home lacks A/C and reached 100F (38C) this summer for an entire week, so I decided to err on the side of too much cooling. The new PC should be a lot quiter than the one I have now, which is quite noisy when its 90mm pull-style fan revs up.

Well, yes. Case fans should move air through a case. Without that, the CPU fan will just circulate the warm air inside the case.