I'm have a project which is using an ATMega 328 which is powered by 5 volts. It is connected to an accelerometer/gyro breakout board through a 3.3 voltage regulator and supplying the 3.3 volts to the ATMega's AREF pin. I want to control a Jaguar speed controller via PWM, which I believe expects a 5 volt signal. My question is, when I set the AREF pin to 3.3 volts, is that going to change the upper limit of my PWM output from 5 volts to 3.3 volts?
AREF is nothing to do with PWM, it's the analogue reference input for the ADC. With a 5V supply, you will get a 5V PWM output.
AREF is defined as as the analog input voltage-reference. I looked in a few places and I can't find any discussion of changing the PWM voltage. Not a definitive 'no' but that would be my guess. I'd be reaching for my meter, right about now.