I found something and now it works for me. I have never coded before so not sure if this is a good practice, but here"s what made it work for me:
go to : usr/lib/pytho2.7/site-packages/configgen/generators/dolphin/dolphinController.py
Edit that file
Around ⅔ of the file, you will see a line : generateControllerConfig_any(playersControllers, “GCPadNew.ini” , (…)
What I did was change the “GCPadNew.ini” to something else, I wrote “GCPadNew.iniFAKE” so that it wouldnt always overwrite the GCPadNew.ini file
After that, I went back to the “GCPadNew.ini” file in userdata/system/configs/dolphin-emu and eddited “GCPadNew.ini”
What I did was swap the b button and x button and also added 2 lines, one for DPad down and Dpad right which weren’t in my config file for some reason
D-Pad/Down = ‘Axis 7+’
D-Pad/Right = ‘Axis 6+’
Hope that works for you, cheers !