You can open "%LOCALAPPDATA%\SuperCrateBoxTogether" in Explorer, open "controls.ini" with notepad, and edit controls to whatever you want.
Is that on Mac or Linux? The path would usually be like /.wine/drive_c/users/<your name>/AppData/Local/SuperCrateBoxTogether/controls.ini. Using directory search would also seem like a good option, as the directory name doesn't change under Wine.
Edit: If that question is about what the format is, try changing gamepad1 to gamepad5 for DirectInput. I'm not entirely sure if this game was compiled with a sufficiently new version of GameMaker to support that though, but worth a shot. In worst case could set controls to keyboard buttons and then run something to map gamepad actions to keyboard.