I've been tracing the APM 2.5's inputs, outputs, and IO pins using the EAGLE files posted in the DIYDrones store. Tracing the PWM outputs back to the ATMega2560 is simple enough as they are directly connected. Tracing the general IO pins back to the ATMega2560 is a bit harder as some attach to both the PWM and the ADC pins on the ATMega2560. Tracing the PWM Inputs back to the ATMega2560 is rather difficult however, as they pass through the ATMega32 first. What is the function of the ATMega32 as used by the ArduRover code? More specifically, how would I write code to access the IO pins? What pin numbers do I use?
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I can't tell you how to access the pins, but I'm pretty sure the ATMega32 is there to convert the input PWM channels into a single serial stream to then feed into the ATMega2560