ABoxwithSWAG: So I saw Witcher 3 GOTY for a really nice price so I went with the GOG version instead of the Steam version. I played with a PS3 controller mapped as an XInput using Better DS3 and it worked. After some time, I loaded up the game and it didn't recognize my controller. I've tried literally everything I could to get it working since I don't like this game's keyboard/mouse controls. I later got a DS4 controller with an official Sony Bluetooth Adapter made specifically for the controller which connects the controller to the adapter which is connected to the computer. This makes the computer see it as a wired connection and not a wireless connection. I used DS4Windows to map the controller as an XBox One controller but it still doesn't work. Both the DS3 and DS4 controller work with all of my steam games using the XInput method and the DS4 controller even works raw, without any external programs, in certain games. I've tried contacting support for both GOG and CD Project Red but I came out with nothing. Please help me and and any questions for details as needed.

ABoxwithSWAG: Thanks but that didn't work. I think its GOG Galaxy because I already uninstalled and reinstalled my game.

Rndysasqatch: It IS Gog Galaxy. There's TWO game overlays that you need to turn off to get controllers working again.
One of them is the main GOG galaxy overlay and the other one is under Thw Witcher 3 DLC
the DLC one was tougher to find. I guarantee your controllers will work once you find both of these overlays and turn them off. Good luck!

ABoxwithSWAG: SOLVED!

I did some digging and I found a few things. When opening up the game controller panel I would see 2 Xbox controllers. The first of which was unresponsive, but the second was the working one. Assuming that the very top one (first listed and unrespinsive one) was considered to be in slot 1 or player 1, I realized that the working controller must be in slot 2 as player 2. This explains why in Rocket League (Steam) when I use my controller it would only register as P2, but if I used my PS4 contorller raw (without the use of 3rd party software because Rocket League has native DS4 support) I was able to play as player one since the top (slot one) controller was my DS4 controller and not the unresponsive Xbox controller. I fixed this by going into device manager and disable the xbox controllers until the only one left was the responsive one, making it P1. I don't know what causes this to happen, but if anyone else has the same issue I have a fix.

Steps:
Connect DS4 (works with new and old DS4 plus the official sont adapter for pc)
Open DS4Windows or InputMapper
Make sure controller has been connected as Xbox controller
Open Game Controller Panel (Start Menu-controllers-enter)
Check how many game controllers are connected (only the ones recongnized as Xbox controllers will work with the game)
Double Click each Xbox controller and check if one of them responsive
If so, continue to the Device Manager (Start Menu-device-enter)
Scroll down to Xbox Peripherals and disable (one at a time) each Xbox controller and reboot as prompted
Open Game Controller Panel and check if the top controller slot is the responsive controller (if not repeat previous step)
Once the Xbox controller on the top of the list is the responsive one, open your game and test it out.

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Original Post:

So I saw Witcher 3 GOTY for a really nice price so I went with the GOG version instead of the Steam version. I played with a PS3 controller mapped as an XInput using Better DS3 and it worked. After some time, I loaded up the game and it didn't recognize my controller. I've tried literally everything I could to get it working since I don't like this game's keyboard/mouse controls. I later got a DS4 controller with an official Sony Bluetooth Adapter made specifically for the controller which connects the controller to the adapter which is connected to the computer. This makes the computer see it as a wired connection and not a wireless connection. I used DS4Windows to map the controller as an XBox One controller but it still doesn't work. Both the DS3 and DS4 controller work with all of my steam games using the XInput method and the DS4 controller even works raw, without any external programs, in certain games. I've tried contacting support for both GOG and CD Project Red but I came out with nothing. Please help me and and any questions for details as needed.

EDIT: It's been over 2 weeks and still no fix. I've contacted GOG and CD Projekt Red, but no solution has been found. I've uninstalled GOG Galaxy and tried downloading Witcher 3 on its own, but it still won't work. I believe something on my computer is preventing this (ex. some file in the game). I've also tried several other tools for connecting my DS4 Controller as an XInput.