I don't have an Nvidia controller, only a Duelshock 4 (the later tablets never came with one). So what I'm about to suggest COULD work, but I cannot guarantee it.
So, what you want to do is download and un-zip the JoyToKey files on your computer and run the JoyToKey.exe file. You can un-zip the files with either WinRar or 7-Zip. Then close JoyToKey properly by going to "File" -> "Quit", once done follow these instructions:
- Launch Citra with the controller paired using the instructions I wrote above. Or, if you know another way to just mirror the desktop on the Shield do that instead.
- Go to your PC and now minimize Citra.
- Re-launch JoyToKey and use that software to configure the Nvida Controller to buttons on your keyboard. You can find out what button on the controller does what as when you interact with the controller, on JoyToKey that key will be lit up with a Yellow outline. This could also be a good time to check if the analogue sticks are configured properly too (one stick not moving all the way right for example), you can do that with the "Configure Joysticks" tool/settings in JoyToKey. i CANNOT give you more help on that software as I don't have the Nvidia controller on hand.
- Once all the buttons are mapped, maximize Citra.
- Go to "Emulation" -> "Configure".
- Go to the "Input" tab.
- Use the Nvidia controller to map that to the 3DS controls.
- Then click "Ok".
- Now feel free to launch your game with the Shield or the PC.
Every time you want to use Citra with that Nvidia Controller you'll need to launch JoyToKey on your computer first. Thankfully, none of the other steps above need to repeated once done.
Also pressing the big red "X" on JoyToKey doesn't automatically close the program. You need to manually close it via the "File" -> "Quit" options in the software.
Oh, as for the mouse movement you could also map that with JoyToKey. OR if the Shield box/controller has some sort of touchscreen functionality (like the tablet) that will work automatically for mouse movement with no configuration required.