Thank you for the quick reply, Atari.
Problem solved, i was just setting the wrong buttons in the in-game control configuration. I’ve set it up correctly and everything is OK now, ES controls are overriden by my custom remaps.
The problem i was referring to is that i needed different button configurations per game or per directory (form example SF series use 6 buttons in a 3+3 layout but KoF series only use 4 in a 1×4 layout) and it seemed to me that ES controller configuration did override my in-game remaps. It was just that i was remapping the wrong buttons, now it works great!
Thank’s again for the quick reply.