Variable Frequency on AVR Chip?
It's not clear, but it seems from your question that you want to have a variable frequency waveform that responds to a Pot value for adjustment.

Just staying in the AVR mode (there are many different ways to do this) you could also do this without changing the operating frequency of the device.  You would just need to read the POT value with the ADC input and use that value to adjust the PWM output accordingly.