Okay, so I couldn't figure out how to do it, so I ended up with 3 different entries in the EmulationStation.
I'm leaving instructions and the *.svg files I made just in case anyone wants to recreate my scenario.

3 Entries on EmulationStation:

FBA Capcom Fighting Games, mapped for SNES-style controllers (4 face buttons + 2 shoulder buttons; 8bitdo SNES sn30, 8bitdo NES n30) FBA Capcom Fighting Games, mapped for Saturn-style controllers (6 face buttons + 2 shoulder buttons; RetroBit Saturn Pad, RetroBit Genesis Arcade Pad, 8bitdo Mega Drive m30, Sega Saturn USB Pad, Retroflag Classic Controller) FBA Capcom Fighting Games, mapped for PlayStation-style controllers (4 face buttons + 4 shoulder buttons; DualShock, DualShock 2, DualShock 3, DualShock 4, Xbox 360 controller, Xbox One controller, Hori Fighting Commander, Hori Real Arcade Pro, Brook Universal Stick or pretty much any arcade stick that follows the standard layout)

That way you can use whatever controller you have available and the button layout will always be correct for those fighting games.

1st Step - Add the Systems on es_systems.cfg

<system> <name>capcomf4</name> <fullname>Final Burn Alpha</fullname> <path>/home/pi/RetroPie/roms/capcom-fighting</path> <extension>.7z .cue .fba .iso .zip .7Z .CUE .FBA .ISO .ZIP</extension> <command>/opt/retropie/supplementary/runcommand/runcommand.sh 0 _SYS_ capcomf4 %ROM%</command> <platform>arcade</platform> <theme>capcomf4</theme> </system> <system> <name>capcomf6</name> <fullname>Final Burn Alpha</fullname> <path>/home/pi/RetroPie/roms/capcom-fighting</path> <extension>.7z .cue .fba .iso .zip .7Z .CUE .FBA .ISO .ZIP</extension> <command>/opt/retropie/supplementary/runcommand/runcommand.sh 0 _SYS_ capcomf6 %ROM%</command> <platform>arcade</platform> <theme>capcomf6</theme> </system> <system> <name>capcomfpsx</name> <fullname>Final Burn Alpha</fullname> <path>/home/pi/RetroPie/roms/capcom-fighting</path> <extension>.7z .cue .fba .iso .zip .7Z .CUE .FBA .ISO .ZIP</extension> <command>/opt/retropie/supplementary/runcommand/runcommand.sh 0 _SYS_ capcomfpsx %ROM%</command> <platform>arcade</platform> <theme>capcomfpsx</theme> </system>

2nd Step - Add the Themes Files
https://www62.zippyshare.com/v/wMXwTxNE/file.html
Just copy to the folder /etc/emulationstation/themes/carbon

3rd Step - Add the Emulation Settings
https://www69.zippyshare.com/v/2HnpWDWb/file.html
Just copy to the folder /opt/retropie/configs
The remap info are in those files. Just a reminder, your controllers have to set according to the wiki https://github.com/RetroPie/RetroPie-Setup/wiki, for instance, the Left Shoulder is mapped to the first button to the left on the top row of your controller.

4th Step - Create Folder and Copy ROMs
You'll need a folder called capcom-fighting and drop your ROMs there.

If you're using Arcade Manager, here's the *.cvs file of the non-merged ROMs I used:

name; dstlku; hsf2; hsf2j; jojo; jojoba; jojobane; jojoj; mbomberj; mbombrdj; megaman; megaman2; mshj; mshu; mshvsfj; mshvsfu; mvscjsing; mvscu; nwarru; redearth; rockman2j; rockmanj; sf; sf2cejc; sf2ceuc; sf2hf; sf2hfj; sf2jl; sf2uk; sfa2u; sfa3u; sfau; sfiii2; sfiii2j; sfiii3n; sfiii3u; sfiiij; sfiiiu; sfj; sfz2alj; sfz2j; sfz3j; sfzj; smbomb; ssf2t; ssf2tb; ssf2tbj; ssf2xj; vampj; vhunt2; vhuntj; vsav2; vsavj; vsavu; warzard; xmcotaj; xmcotau; xmvsfj; xmvsfu;

Also, EmulationStation doesn't seem to respect any order other than alphabetically, so I numbered the games in my gamelist.xml

Well, that should be it. Unfortunatelly it won't let me play fighting games against someone who owns a different controller than the one I decide to use, but at the very least I have everything mapped and ready for use.

Also I am aware that Street Fighter The Movie runs well and uses a 6-button layout but... I guess I rather not remember that exists.

@bc320 I'm with you on this. With such a versatile machine like the Pi (any model) you don't know what you'll be using it some years into the future. Furthermore, Retropie runs on Linux which uses free memory to buffer I/O operations to speed up file access etc. You can see the memory allocation with the command free -h.

@arduinoGamepad Emulationstation is using SDL's joystick sub-system to handle joysticks, my guess it's not detected as such. There's a similar sdl-jstest utility -which is similar to jstest - that tests whether the joystick is detected by SDL.

To get it detected by ES, try one of these - in order

add a local udev rule to force the device to appear as a joystick: SUBSYSTEM=="input", ATTRS{idVendor}=="<VID>", ATTRS{idProduct}=="<PID>" ENV{ID_INPUT_JOYSTICK}="1"

substituting VID and PID with the values you get for your controller from running lsusb.

Use Xboxdrv to make your device be seen as an Xbox driver.

@Nightfire Just noticed your question been a while., but I have to do this in my gpi case.

Controls

Joystick axis Should just work
joystick_1_vert joy0 axis1
joystick_1_horiz joy0 axis0

In Game Buttons
left_button_1 key32 joy0_1
right_button_1 key109 joy0_0

Start Buttons
Colecovision has a numeric keypad to start game 1-9. Also *, 0 and # Key.
This is where jsTest comes in handy. The # from jsTest should be appended to joy0_

key1_1 key49 joy0_7
key2_1 key50 joy0_6
key3_1 key51 joy0_3
key4_1 key52 joy0_2
key5_1 key53 joy0_4
key6_1 key54 joy0_5
key7_1 key55
key8_1 key56
key9_1 key57
key*_1 key111
key0_1 key48
key#_1 key112

key_save key1073741882 joy0_6 joy0_5
key_restore key1073741883 joy0_6 joy0_4
key_exit key1073741939 joy0_6 joy0_7
key_pause key1073741884
key_reset key8
key_screenshot key1073741891

https://sites.google.com/site/gregsqna/gaming/handhelds/retroflaggpi/emu/colecovision

Thank you,
I tried this and I found that the sound gets very choppy in FinalBurnNeo playing Street Fighter III.
Thanks anyway.

this should work

Ok.
I read it to mean change the file name in just the m3u file.

It's not only RetroPie that changed over the years, but also prboom. There's now a core option for the FPS (I think the original Doom ran at 30 or 35FPS), check if yours is set to 60 FPS.
Also, when opening a help topic, please add more info about your system and setup, as detailed in https://retropie.org.uk/forum/topic/3/read-this-first.

It seems to download fine for me. We've had a few complaints over time with similar symptoms, it's usually something ISP related. Try downloading from another location or try a torrent download.

@jodiefoster said in Custom Folder Question Help Needed Urgent:

i looked into the .dat and no information is their about region such as usa or bra or ita.
can you give me more info regarding this

I was under the impression that some .dat files contain also country info, I guess you'll need to filter them normally - via clrmamepro or similar programs.

You can use symlinks instead of creating empty files - they don't take up space and they appear as regular files..

https://en.wikipedia.org/wiki/Symbolic_link

@bejhan this didnt fix the black screen issue for me with kodi 18.1 on this vizio vo400e tv. This did fix an issue with kodi 18.1 where the screen was crazy zoomed in and the only way to fix it was to minimize the screen and then maximize it again on an lg oled c6.
On the vizio tv that i am having issues with now if i just power the tv off then on again it works fine till i go back to the retropie menu and then thats a black screen. Same thing happens if I switch film mode off then kodi appears but then when you exit the retropie menu is a black screen. Same thing happens when you switch inputs on the tv from hdmi 1 (where pie is connected) to something else then back to hdmi 1 and once again when you exit the retropie menu is black screen until you do 1 of the methods i mentioned above. So what is kodi on launch (and exit) doing that is making the tv black screen that nothing else installed in retropie is doing. For example I have pixel desktop (lxde) installed under ports also and a bunch of emulators. Everything else but kodi launches and exits fine.

We don't support 3rd party images - https://retropie.org.uk/forum/topic/3/read-this-first. You already opened this topic a few weeks back and from what I've seen, there's more than just the pi2scart that's configured on the image - including RetroArch.
You can either start with a stock RetroPie image (and configure pi2scart only through /boot/config.txt) or use ask the image authors for guidance.

@Darksavior awesome. Thanks for the help.

Have done now. Its giving me no errors. Guess I will just have to reinstall and see if that fixes it. Thanks for your help.

See here: https://askubuntu.com/questions/47642/how-to-start-a-gui-software-on-a-remote-linux-pc-via-ssh

I have tried FCEUmm (SVN) 1613c58 and Nestopia 1.49-WIP 54f6d76. Both work with ordinary mouse, but not this one.

@mitu edit: duh got it. Thanks again.