se either the keyboard or an external gamepad. In terms of the touch controls for the lower screen, you can use the mouse directly to click wherever you want.
Citra supports a ton of games from the Nintendo catalog in both 2D and 3D, though the emulator particularly shines with the 3D titles, allowing for a more intense resolution that completely transforms some games, making it seem like they're not even from a handheld device. Pokémon Sun and Moon and The Legend of Zelda: A Link Between Worlds, for example, look amazing.
Citra is possibly the best and most advanced Nintendo 3DS emulator you can find. It's an open source project created by volunteers that lets you enjoy your handheld games on a desktop computer.