Tom, thanks for this! Now I understand. I thought since I'm programming the atmega then pin numbers would be its pins. How in the world would a newbie manage to find, or even know to look for, that document? I'm an old guy and not very good at finding stuff online as opposed to having a printed manual to read through.
I will annotate my schematic as such. They could perhaps have silkscreened these pin numbers on one side of the "AD" connector body and left A0...A5 on the other side; might have helped. As for the schematic, these numbers should be added to the right of the AD connector, as they are for the other two connectors. Suggestion to Arduino.
Again, thank you very much!
Now I can start to debug actual code!