Same as in any other classic FPS, the N64 has four C-buttons for directional control in addition to the stick. By default however it uses a Doom1/Duke3D-style control scheme, not a modern one, meaning the stick doing forward/backward/turn-left/turn-right, while the C-buttons are doing look-up/down and strafing. Modern games just switch the turn and strafing around.

That said, Goldeneye, along with Perfect Dark, both have numerous alternative control options, one of them is using two gamepads, so you can have two analog stick and control it just like any modern shooter. N64 controller is pretty unique in being usable with only one hand.

In the default layout the analogue stick controlled forward and backward movement and turning left or right. The yellow c buttons could be used for strafing or adjusting the vertical "aim" (the game heavily relied on autoaim). It was also possible to use the R trigger to enter an aiming mode where the analogue acts like the left stick would in modern FPS.

There was an option to use the c-buttons like WASD and the stick to aim but judging from the way people talk about goldeneye a lot of players never discovered it.

you would hold the R trigger down to aim and it would switch from walking/move to a superimposed crosshair you could aim with the joystick. I think you could also just hold trigger and shoot without aiming. That's how I recall it worked at least