Update
Yesterday I went ahead and FTP'ed the retroarch.cfg to this folder on the SD card:
\retropie\configs\from_retropie\configs\all\retroarch.cfg
-- Note to be honest I am at work and not in front of the RPi3 so I am guessing that was the path to the file.
I rebooted the Rpi3 and went down to the game-room to see what the controls now did. Well they worked! They all did something and that was great. No they are not all correctly mapped to the MAME/iPAC2's default settings. One example of an issue is that in MAME to exit MAME you traditionally do a P1 & P2. On this current button configuration I have to do a P2&P1. This will need to be changed in the config.
I also noticed that Player 1's buttons correspond to getting into and out of menus. I will need to disable those menus and the white dialog config box in the end.
Otherwise MAME setup is looking good!
One question is this can I create a retroarch.cfg file for just the MAME versions I am using and let the original mapping work for all other consoles? What I eventually want to do is to have matching USB joysticks on a hook on either side of the cab in case I want to hit some SMB3 or old school SNES game.
Thank you,
Battlecat