Controller doesn't work with Steam Big Picture running

[mdueck]

Question: Can I completely disable Steam remapping my controller buttons when Steam Big Picture is running?

Context for question: I've added BigBox as a non-steam game so that I can play my emulated games on my TV using my steam link. In steam big picture I disabled steam remapping my controller buttons with BigBox by using the settings pictured here. I didn't quite understand each of the settings, but I kind of guessed at what to disable and it worked.

Two of my emulators and games work perfect when I open them by going: Steam Big Picture > BigBox > both Dolphin and SNES9x

However I'm getting an issue with my controllers when I try to use a frontend for mupen64plus called m64p (https://m64p.github.io/). I have the controllers working on PJ64, but there are some issues.
If I could solve either of my issues for my N64 emulators then that would be great.

m64p

The controller configuration works when I open the emulator through BigBox from my desktop, but not when I start out by going through Steam Big Picture.
Is there someway to completely disable the Steam remapping of my controller buttons?

PJ64

I opted to work with m64p instead for two reasons:
1. I want to run BigBox and all my emulators on my 3rd monitor. My primary monitor is 16:10, but both my 3rd monitor and my TV (connected to the steam link) are 16:9. PJ64 will only go fullscreen on the primary monitor (16:10) though, so I get black bars on the sides of my 16:9 TV when I use this emulator. I did a lot of looking around the internet and I don't think there is a way to play PJ64 in fullscreen on a monitor other than the primary one.
2. PJ64 gives this error when I try to open it with Steam Big Picture running if I don't remember to first turn off my Steam Controller. When I forget then its not just simply try again, the error persists until I stop streaming my desktop then start all over again. 

Retroarch:

I put a couple hours into working with this emulator, but I can't get the controllers to work properly either. Not sure if this is my best bet, but I didn't want to keep sinking time into it.

 

 

Edited May 23, 2020 by mdueck