I have only looked really closely at the PCA module available on the Cygnal parts. When you use the PCA for PWM outputs you have threee choices of how to make it work.

8-Bit Mode
There is an 8-bit PWM mode where once the parameters are set the waveform generates without further software intervention. You get a little leeway on determining the period of the PWM waveform in that the core timer of the PCA is driven at a clock rate that one can select from several choices. One of the choices is the Timer 0 overflow which gives the greatest degree of control. However with any clocking selection the PWM period is 256 counts of the PCA main selected clock.

16-Bit Mode
In the 16 bit mode the PWM parameters are set by software once each pulse cycle time. Thus software is involved in setting a new compare value after each time the output toggles. It is not necessary to service the re-load values more than once a PWM cycle and if you do it properly it should be possible to update multiple PWMs in a single interrupt service routine. This mode also has the same clocking selections for the counter rate to use but the period is now 65536 clocks.

High Speed Mode.
The PCA also supports a mode where the output pin can toggle state at each match compare time. Usingh this with a more robust software involvement it is possible to create a PWM output that you get full control over the period as well as the duty cycle. The nature of the design of the PCA is that the match compare interrupt happens after the output pin has toggled. This permits waveforms to be generated that have no jitter from software interrupt latency issues. You are however then limited to a high or low time narrowest width that relates to the interrupt serviceing routine worst case latency time plus the service routine execution time.

Hope this helps clarify. Not PCA's are exactly the same so the one on your derivative may vary a little.

Michael Karas