For the mapping problem, there is no need to delete any files. Simply do the following:
Start playing game. Bring up options menu. Go to Configuration. Go to Configure Controllers. Now configure your controllers the way you want them. Exit back to the game. Settings are saved automatically for the game. The next time you play that game, the controller settings you just specified will be used.
Alternately, you could, from the main menu, select "Configure Game", select the game you want to configure, and redo the controller settings from there. Same thing.