Okay, I tried reading through the wiki, and I couldn't figure out what they were trying to describe. I ended up getting the button numbers of the n64 usb controller, which is labeled as 'Dragonfire xxx' on screen and in console.
I went in and modified InputAutoCfg.ini and it looks like this now:
http://pasteat.me/view/36ecac29
(I could probably remove all the controllers except the dragonfire one, but this file is written by ES so it would probably add them back in once I configured a new input.
I also pasted in my retroarch.cfg file in there. I couldn't find out in that file to explicitly map my buttons to the individual buttons for n64, and had no idea what the property name needed to be to assign the value. With that, I also don't know how to tell the retroarch.cfg file to only use those mappings on the Dragonfire (n64) controller.
In what I have now, the hot keys at least work (Start + Z) to exit the emulator, but the rest of the buttons are not mapped correctly.
I set the default emulator for n64 to lr-mupen64.
Could you offer me some advise, please?