Setting the PWM frequency to 25kHz - Arduino Due

The "pwm01.h" library will accommodate your needs. Library, instructions and example in link below. The function "pwm_set_resolution" sets the resolution in bits. If needed, you can setup two separate PWM frequencies in the same program. Good luck.

http://forum.arduino.cc/index.php?PHPSESSID=povm0bi5ipfp6s6o33a226h4s0&topic=144446.msg1149044#msg1149044