Why do you feel you need to change the PWM frequency?
You can power the Arduino from the same 12v source as your motors. Connect +12v to the Vin pin or to the DC power jack.
As for PWM frequency I don't think there's a specific library but it can be done by reprogramming the relevant timer module directly. If you want millis() and micros() to still work don't modify timer0.
the jeremy blum arduino tutorial on youtube on motors and PWM might be of use too you.