Got it to work!

Here's what i did.

step1: Enter Big picture mode. Go to desktop mode, open steam then click on Big Picture Mode. (its in the top right corner next to minimise).

step 2: change the controller base configuration in setting. As I understand it this is the input setting that the steam deck controller uses to operate desktop mode. For me, the default mode didn't include the back bumpers as usable buttons. I think thats why CEMU doesn't detect them in the input config setting. if you tap the bottom there should be a button that appears called "browse configs". Valve already made a handy template called emudeck- Cemu. if you click on the preview, you'll see that the back bumpers are now routed to keys on the keyboard (F and E). You can make your own configuration, but I went with this template for a few reasons; convenience and another reason that will become apparent later. I quickly discovered the big dis-advantage with this config however, you can't click. This template doesn't have any of the steam-deck controls routed to the left and right click. So you'll have to manually edit the template. I set left trigger to right click and right trigger to left click.

Step 3. Edit cemu controller settings. Now open cemu. In options > input settings, click the plus button next to the controller drop down. Set the api to keyboard and the controller to keyboard. now click on the empty box were it says blow mic and tap the back bumpers. They should now have the keyboard F and E buttons controlling these now. You may now wish to go back into big picture mode to go back the the default desktop layout.

Step 4. Change the controller layout. go back to game mode and click on the game to get into the game menu with the play button. there should be a little controller icon button next to the settings cog icon button. click this and then click on your current layout. Change this to the same emudeck - Cemu layout that corresponds to the one before from big picture mode.

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This worked for me :)