ok i found a way to remap 3ds button, 3ds button refer as 0, 1,8,9 for a,b,x,y(not in that order) and l,r as 10,11, no idea which number for zl and zr, so you have to put according button number in the bracket of the corresponding button in retroarch config file, you can find it in CPS Forwarder Creator 1.5.3\tools\assets_cps1\retroarch.cfg for cps1 game or CPS Forwarder Creator 1.5.3\tools\assets_cps2\retroarch.cfg for cps2 game.
as exemple for street fighter, I switch L/R button with with Y/B (low punch/kick), so i change mapping like this
input_player1_b_btn = "11"
input_player1_y_btn = "10"
input_player1_a_btn = "8"
input_player1_x_btn = "9"
input_player1_l_btn = "1"
input_player1_r_btn = "0"