For the wired Consoles an original playstation 3 controller can be connected to retropie using the following steps:
1) Connect the playstation controller to the console using a USB cable
2) Let the lights blink on the controller for about 5 seconds and then disconnect the USB cable from the controller
3) Keep the Playstation3/HOME button pressed and till the controller is paired.
4) Finish the key mapping for the new controller by using an existing wired controller, press Start >> Configure input
Please note for wired console, only original sony playstation controller can be paired.
For wireless consoles only the controller sold by the retrogamingconsoles store is applicable.