Hi, FS-UAE Arcade uses the same config file, but does not allow overriding covers. FS-UAE Arcade 3.x only works with content from the online game database. Maybe that's something to improve for FS-UAE Arcade 4.x.
Regarding gamepad usage: as long as the gamepad is recognized properly, it should be usable for navigation. My guess is that you need to use FS-UAE Launcher -> Settings -> Controllers and map the buttons first.
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