David Brownell wrote a basic driver for the built-in PWM controller on AP7000 and posted it to the mailing list. To try it out on the STK1000, apply the following three patches:
Now, make sure SW3 is in the default position and connect some long jumpers from J29 pins 13 (pwm2) and/or 16 (pwm3) to some unused LED pins.
To use it for other purposes on your custom board, patch #3 above may serve as an example on how to hook everything up. If you need to write a custom driver (i.e. you have something different than a LED that you want to control), patch #2 may serve as an example on how to do that.