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The Retroarch configuration will only work with the libretto emulator, which in my experience, is not optimal for N64.
You can modify/edit/check the Retroarch config – it is kept in opt/retropie/emulators/retroarch/configs/ (I think – I cant check, as I’m on the road). If you use the MUPEN64PLUS emulator, then the config file is in the InputAuto.cfg or maybe I got it backwards and it is AutoInput.cfg. Anyway, that file is in the opt/retropie/configs/n64/ folder.
To figure out the EXACT name of your controller (so you know which configuration to edit), from the terminal, type
jstest /dev/input/js0 (and check your button map while you are there).
Hope this helps.