Well, starting off the ps3driver is pretty good and if you want the default Hotkey(PS_BTN)+Start then this won't be a problem;
However if you want to assign custom hotkeys to retroarch, if you do this with the controller plugged in, it will assign the button number manually and these will differ than if you connect wirelessly with the ps3 controller. You can always press start on a retroarch option to reset it to its default(auto) value, where it will find the start and hotkey buttons automatically and not reference an arbitrary button number from its disconnected duality.
There is a solution to this without transcribing the root configurations to bend the systemdaemons to your will.
In the RetroPie management package drivers there is an alternative, the sixaxis helper driver. Installing this will uninstall the ps3controller driver and replace it. The arbitrated button numbers for wireless and connected will be as one and you can configure input mappings peacefully.
