CPU fan does plug into cpu header. Probably not such a good idea to plug two fans in the system fan header. The combined current draw may exceed the boards rating. In other words, smoke might leak out of the MB. Better idea is plug one in the board. The other in an available molex connecter from your power supply.
I've also noticed (just read some more of the manual online) that both headers on the mobo are 4-pin. Is it true that most chassis fans are 3-pin? So the motherboard cannot control the chassis fans even if you plug the fans into it?