If you want the east button (A-Button on SNES-Pad = Circle on PSX = B on Xbox Pad) as select button in EmulationStation and south button (B-Button on SNES Pad = X Button on PSX = A Button on Xbox Pad) as exit/going backwards in the Menu, then you can change to this by going to System Settings, Developer, Switch A/B Buttons in Emulationstation)
The concept of Batocera is, that you only have to configure your Gamepad once in EmulationStation under Controller Settings, Configure A Controller (at least if it is not already pre-configured out-of-thebox) and then all button-mapping configurations for every system (SNES, Gameboy, Playstation, MegaDrive etc.) will already be preconfigured in a proper way, without having the user to configure all for themself.
When configuring your pad be aware, that the buttons, which you are asked to press, refer to the design of a SNES Gamepad. So for example if the button mapping asks you to press A, then press the east-button on the controller/pad you are using (on an Xbox controller this would be B then).