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
Some rules of thumb:
Analogue stick -> left analogue stick
Z & R --> triggers
D pad -> D pad
L -> select button
And then, map A and B and the bottom right two C buttons to A B X Y, and then the top right C buttons to the shoulder buttons.
But you're going to want to change that based on what game you're playing. For example the Zelda games might make more sense with the C buttons using A B X Y, and then the A and B buttons getting remapped to triggers. For Mario 64, I map the C keys to the right analogue stick. On a lot of games I will use the right analogue stick for the analogue stick, as I'm more used to aiming with that (starfox, rogue squadron, turok come to mind).