These are my preferred settings for Citra.

Playing 3DS games on a single screen can be tough. The vertical form factor of the 3DS makes gaming quite the challenge when emulating. So, these are my preferred Citra settings. Feel free to use or improve them.

Picross 3D

• Main screen: bottom
• Other screen: small or disabled

Use a mouse and keyboard for this one, with d-pad and L buttons being used for controls. Other screen is not required.

The Legend of Zelda: A Link Between Worlds

• Main screen: top
• Other screen: small

Touch screen mappings should be used for bell (fast travel) and equipment. The map is on the other screen, so it should be visible. Map d-pad to right stick for camera control.

Stella Glow

• Main screen: top
• Other screen: small or disabled

Almost everything happens on the top screen. Map d-pad to left stick and circle pad to right stick for camera control.

Shin Megami Tensei: Devil Survivor Overclocked

• Main screen: bottom
• Other screen: small or disabled

Almost everything happens in the bottom screen, but the top screen is used to see stats, so it still might be useful.

Puyo Puyo Chronicles

• Put screens side by side

Cutscenes and overworld are on the main screen, but actual battles (and the map) are on the bottom screen, so you’ll need either both side by side or switch frequently.

Shin Megami Tensei IV

• Main screen: top
• Other screen: picture-in-picture

The top screen is used for dialogue, cutscenes and the overworld, while the bottom screen is used for the map and menus. Using picture-in-picture should solve this conundrum for the most part without the ugliness of side-by-side.