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You can setting up your Controller in the menu
Input settings. You can add up to eight controllers to the emulator.
Wii U Gamepad
Wii U Pro Controller
Wii U Classic Controller
Supported input devices
Xbox 360 Controller (USB)
Setting up the xBox 360 Controller (same for both wireless and wired via USB)
Open up Cemu, head to the Input section, select "Emulated Device" either as WiiU GamePad (recommended) or the WiiU Pro Controller.
Next up select "Controller API" as Xinput and then select your controller in the drop down menu (most likely it will show up as "Controller 1" unless you got more connected.
After that you can click the gray area next to the "A" button and start mapping your controller as you like. It will automatically jump to the next input for you. Once this is done you can hit "X" in the top right corner and you're pretty much ready to go!
Official Wii Controllers
Refer to the Motion Sensing page for several solutions involving providing motion data to Cemu.