So I use a set up like in pic related. The top screen I use on my main monitor, and the second touch screen I put on my iPad through and app called Duet Display, which also allows touch screen. To get it like that I put the screen display to Side by Side, and then just drag the window halfway on one screen and half way on the other.
My suggestion is to allow both screens to be split into different windows so you can have on window on full screen on one monitor and the other fullscreen on the other monitor. This would be better since we mainly use the top screen and it’s better to play in full screen while rendering it in 4k.
And render the game in different ratios like 16:9 or 4:3 etc… so it actually takes up the whole screen instead of having black bars
And I don’t know if the next suggestion is realistic, but perhaps Citra can have a companion app which connects via the hone wifi which you put into your iPad or phone, and you can use it as the 2nd touch screen