I’m having the same issue (not able to get the PS3 controller to configure on the Emulationstation GUI) but I got it working in a way that I can use it to play games though you still would have to use a keyboard to access the content on the Emulationstation GUI.
-On the RetroPie Menu
-Configure RetroArch / Launch RetroArch RGUI
-Input User # Binds
This way you would be able to play the games but still there is the issue with the PS3 controller not working on the EmulationStation Gui.