My only concern over connecting all fans to the board would be power handling. I know my Maximus IV Gene-z seems to use the same controller for all 3 plugs(it almost seems like they are already split).
As long as the fans do not draw too much power you can certainly do it that way if you wish. If all fans had been pwm, splitting is quite a bit more easy since they actually use 12 volts and just get a speed signal from the board.
I am not sure if the board will control the cpu fan if it is just a 3 pin one.