In terms of the file being overwritten – as long as you dont reconfgiure your controller each time it should be fine. Just update the file as above, save it (maybe open it up and make sure changes are in there) and remove any controller files you dont need including the .bak. Then when you reboot it should go straight into ES – does it ask you to reconfigure the joypad? Do you update it via SSH?
RetroPie help guides --> https://goo.gl/Yfy8kj
Please read this before asking for help --> http://goo.gl/eLErnl