Two d-pads, one analog stick, three triggers and two face buttons? What were they smoking in Kyoto in the early 90s 
I have only seen a Nintendo 64 in real life like twice back in the 90s so I have no clue what all these buttons do in most games.
Thanks to recent developments I went and downloaded every Nintendo emulator I could. I was surprised to see how fractured Nintendo 64 emulation seems to still be on PC. I was expecting there to be a Duckstation, PCSX2 or Dolphin equivalent but no, there seems to be no clear winner, and two of the bigger ones are closed source and use plugins like it's 2005, and one doesn't even come with a GUI by default
They designed it assuming that you would either use the D-pad or the joystick. Nintendo didn't imagine a world where every controller had two sticks and a d pad and players used all of them at the same time.
Anyway, assuming you're on a modern controller, D pad goes to D pad, joystick to left joystick and C buttons to right joystick. A/B are A/B or possibly B/A if you like, triggers are triggers and Z is left bumper.
Even during the n64 games required all of these. That said it's not too hard to map goldeneye to a switch using the double controller style.