@Finndersen should be in /opt/retropie/configs/all/retroarch-core-options.cfg

I'd recommend using the configuration editor to manage your configs:
https://github.com/retropie/retropie-setup/wiki/Configuration-Editor

You may want to check your system specific retroarch file isnt holding a mass of non-required configs now, there is usually just 4 or 5 lines in there.
A bit like this:
http://pastebin.com/n5FbDBUK

Figured it out!

input_map[p1_doubleleft_up] keyboard[0,8_pad]

etc.

Haven't tried it myself, but here you have a tutorial https://www.lexaloffle.com/bbs/?tid=3935

@BuZz im sorry!! thank you very much!!

@DanC_1987 You need to install the ds4drv ps4 driver still.

https://pypi.python.org/pypi/ds4drv

Problem is.. without the driver, it says 1 gamepad detected.. but can't be configured. With the driver, 2 gamepads detected.. it configures in the "main menu" setup, and can then navigate through emulationstation... but then it's unresponsive in games.. "controller not configured" message after starting any game.

I've read that updating all binaries and scripts should fix it, but it didn't. I still have a controller that navigates through emulationstation, but completely unresponsive in games. Seriously frustrating.

Long update, but I resolved this issue using the Mayflash Wireless Sensor Bar (https://www.amazon.ca/Mayflash-W010-Wireless-Sensor-DolphinBar/dp/B00HZWEB74/ref=sr_1_3?s=electronics&ie=UTF8&qid=1525130286&sr=1-3&keywords=mayflash+wii), which circumvents the pesky control configurations.

Thanks, everybody!