There is a good post that talks about how to hookup multiple PS3 controllers in RetroPie using Bluetooth. I just spent some time getting it to work, and found some steps that need fixing:
When you configure the controller with the actual emulators, the commands should be:
cd ~/RetroPie/emulators/RetroArch/installdir/bin
./retroarch-joyconfig -o p1.cfg -p 1 -j 0
./retroarch-joyconfig -o p2.cfg -p 2 -j 1
cat p*.cfg >> ~/RetroPie/configs/all/retroarch.cfg
sudo nano ~/RetroPie/configs/all/retroarch.cfg
There is also a typo, so when you check the retroarch.cfg file, make sure the last lines for P1 and P2 are:
input_player1_r_y_minus_axis = "-3"
and
input_player2_r_y_minus_axis = "-3"
Okay, hope that helps some people who may be confused, and if I’m wrong on any of these points (I very well could be) just respond below or message me. Also, I appologize if this is in the wrong section; if it is I’ll gladly move it.