Well, you guys are awesome. Once I figured out where to change input settings in Retroarch..and then how to save my configuration...I got it working. The mappings for the left analog stick were blank, somehow. Note: I edited the main RetroArch config, and not Core configs. Both were blank, but I wanted it to correct every N64 rom.
I assume that means the Dpad was working, and it just wasn't being needed by Mario64, which I was testing on.