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
The d-pad is almost never used, so don't worry about it. The L-button also normally doesn't get used. The yellow C buttons are often there to control a camera if you're playing a 3D platformer, so assign it to a right analog stick.