I was finally able to set it up.
I configure the control the best that I can in Emustation.
With HotKey is the Cpad UP
And then I put this configuration in Retroarch.cfg in the N64 folder.
Settings made here will only override settings in the global retroarch.cfg if placed above the #include line
input_remapping_directory = "/opt/retropie/configs/n64/"
input_player1_joypad_index = 2
input_player1_r_x_plus = "8"
input_player1_r_x_minus = "3"
input_player1_r_y_plus = "9"
input_player1_r_y_minus = "0"
input_player1_left = "left"
input_player1_right = "right"
input_player1_up = "up"
input_player1_down = "down"
input_player1_a_btn ="nul"
input_player1_b_btn = "1"
input_player1_y_btn = "2"
input_player1_x_btn = "nul"
input_player1_start_btn = "12"
input_player1_l = "4"
input_player1_r = "5"
input_player1_l2_btn = "6"
#include "/opt/retropie/configs/all/retroarch.cfg"