i've been ripping code out from two of the examples in Atmel Studio .. best sources so far
(adc/pwm example & the synchronous pwm examples)
and re reading the data sheet a couple hundred times ...
i had found that there is a lower limit of time the pwm will work at ..
but don't have the code any more it morphed into other things ... took some experimentation ..
I'm using the pwm/adc with the PDC (sampling bursts of 5636 samples in ~15 ms every 25ms or so ) still adjusting the timing & have put off futher work till i get new sd card shields