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Thank you for your interest in the Intel Aero drone.
The processor GPIO's can be accessed through software.
You can find a guide here on how to access them: https://github.com/intel-aero/meta-intel-aero/wiki/94-(References)-Sensors-GPIOs-LEDs-CAN-bus#processor-gpios
You can also find more details in the hardware guide: https://www.intel.com/content/dam/support/us/en/documents/boardsandkits/aero/intel-aero-compute-board-guide.pdf
As for your second question,
You can configure the PWM signals via the FPGA.
There are 2-byte frequency registers to configure each PWM output. Register value = 25MHz/Desired PWM frequency,
To set PWM0, for instance, to a frequency of 500Hz (2 ms) and 50% Duty Cycle (1 ms), the frequency register should be set to a value of, 25,000,000/500 = 50,000 which is 0xC350.
You can find more info about the FPGA on our wiki: https://github.com/intel-aero/meta-intel-aero/wiki/95-(References)-FPGA
The sample application can be used to configure this.
spi_xfer -b 1 -c 1 -d 5097 -w 2 spi_xfer -b 1 -c 1 -d C398 -w 2
Hope this helps.