you can choose whatever mapping you want. You can have player 1 start as the up control if you wanted.

Map what feels comfortable – you can remap per emulator on top if needed (https://www.youtube.com/watch?v=liJKFUZX4PM) – you can see on the retropie wiki for each system how the retroarch buttons map to each controller to work out what might be best for your xarcade stick.