The N64 controller is the hardest to config because of it’s shape and the C-Buttons. Basically, the C-Buttons can either be camera control (which makes sense to bind them to the right analog stick) or various actions in other games (which means the N64 pad becomes a 6 face buttons pad) so that complicates things.
As a default i bind the C-Buttons to the right analog. Then the digital shoulders to L+R and Z-trigger to the left analog trigger. N64 “A” is 360 “A” and N64 “B” is 360 “X”. Y and B on the 360 pad aren’t used.
This works for me and i don’t mind doing actions in some games by pushing a direction on the right analog stick. Also, most of the time i don’t change the controls per game through RetroArch, i keep the same setup and change the controls by the in-game menus. Many N64 games have control options themselves and it’s usually better to configure them from there.
For FPS games like Goldeneye you might want to make new configs though.