To the question in the title: Yes, through software (specifically "Smart Fan 2" under "GIGABYTE EasyTune"), you can set fan profiles for each fan connected to the mobo. You can also download other fan controlling software if it doesn't work how you want it to.
To the second question: No, unless you want them to be automatically controlled, and to do so, the fans and the fan header have to be PWM.
As a side note, it's PWM (Pulse-width Modulation), not PWN.