Your project already includes the Arduino Mega2560 module A1. Do you want me to also add the bare MCU ATMEGA2560-16AU (TQFP-100), or stick with the module?
All GPIOs are wired to the Net Portals. But the names/designators of these Portals are empty so you can fill them in as you prefer. You probably will don't need them all, so you can delete unused ones or leave them blank.
vasy_skral