SOPC builder

I haven't looked at that PWM yet, but like most PWM circuits you can usually program the period (frequency) and the duty cycle. So the interface is usually a couple of registers that get wired up to Avalon, and the rest is just internal logic that creates the new clock.

As for your idea of creating a clock with a timer..... it will not be clock cycle accurate, and do you really want to be using the processor for creating clocks or processing?

So I would recommend Fischer's steps that he outlined.