A motherboard fan header has between 20 and 40 Watts maximum and if you plug only 2 fans into one fan connector you should be fine since one fan has about 2-5W of powerconsumption.
Also you can plug the 3 pin and the 4 pin fans into one connector, the 4 pin will be pwm controlled and the 3 pin will run on the 12vDC standart voltage.