You'll get a new ini file and xinput1_3.dll in the folder you put x360ce.exe. Rename it to xinput9_1_0.dll and put it in \Steam\steamapps\common\Joe Danger\Bin. Make sure to back up the old file. Also make sure you copy the new x360ce.ini to that folder.
You don't need to do anything with x360ce.exe afterwards.