This section has a few guides written out that are specifically for third generation (TMU) devices. Some of the knowledge may be transferrable to second generation devices.
This image is an overview of the GPIO pinout of the 3rd generation (TMU) AutoPi.
Pins marked with "in use" cannot be used for anything else. This will interrupt the functionality of the AutoPi. This I2C bus is used by the AutoPi, but can be shared with other devices.
All other pins are free and their functionality follows that of the Raspberry Pi.
If you'd like to discuss this topic with us or other fellow community members, you can do so on our community page dedicated for this guide: AutoPi GPIO Pinout
This is a picture of the location of the 5V FORCE pins. You can put a jumper on these pins to prevent the AutoPi from going to hibernation. More info here.