Oh I think I got it. Here’s what you need to do:

You have to set up hotkeys byadding the following lines to the config file.

input_enable_hotkey_btn = “8″
input_exit_emulator_btn = “9″

Now you can press and hold select and press start to exit an emulator with the controller. If you are in an emulator press and hold select and press F1 (keyboard). Now you can go in settings and input settings and remap the B and Y buttons. You will also need the remap the select button to the select button on the controller (should be button 8 I think). now go back and save the new config. It will be saved to another file than retroarch.cfg.
Finally you need to exit the emulator and go to the command shell by pressing F4.
Now go to the config folder:

cd /opt/retropie/configs/all

rename the retroarch.cfg to retroarch.cfg.bak2 (backup):

mv retroarch.cfg retroach.cfg.bak2

and rename the new config file to retroarch.cfg:

mv ????.cfg retroarch.cfg

(I forgot what the new config file was named… something with ???_libretro.cfg)

I should work…. if not, try to change the mapping like above.