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Final Update:
I cant believe I managed to solve this on my own. Who wouldve known the Pi was such a great teaching tool!
Anywho, here is the solution for myself and anyone else who may be stumped about this.
Basically, whenever you manage to open up RetroArch with the F1 hotkey/whatever hotkey you set and whenever you remap everything through it, it will save a .cfg file to /otp/retropie/configs/all. (From what I noticed, depending on which emulator you chose, the filename will be different, so the filename I am using has come from the SNES emulator). My particular file went something along the lines of libretro-1.cfg, and I made a second, more optimized verison which covers both 1p and 2p and, after clicking save, it was saved in the same directory under the filename libretro-2.cfg. You’ll know when it saves. It will show up on sccreen.
Now, exit back to EmulationStation and then hit F4. Once you are jacked into the matrix terminal, type cd /opt/retropie/configs/all. It should see that directory. Type ls to view all of the files in there, just as a refresher.
Now, we must rename and overwrite retroarch.cfg!
I used this to find out how to do that, and I’ll explain it here too: http://www.cyberciti.biz/faq/linux-rename-file/
Anywho, just type in the following, replacing the [] with the name of your file. DO NOT LEAVE THE BRACKETS IN THERE, ITS JUST FOR SHOW OVER HERE. NO BRACKETS ANYWHERE IN THIS LINE OF CODE.
mv [yourfilename.cfg] retroarch.cfg
thats it! it should work across all emulators, so set it right the first time and, if needed, edit it and then go back and “mv” it out again. Cant believe I could find such a simple solution to this!
*protip: with my Logitec F310’s, I managed to set the center Logitec button to toggle the RetroArch menu in case if i needed to speed-change something or if I needed to simply exit the emulator. If you have a similar controller, try it out!