By default the deck functions as keyboard and mouse while in desktop mode.
I believe if you hold the menu button (3 line button) for a couple seconds it's supposed to swap between desktop controls and being a controller.
If that doesn't work, you could possibly try launching Lutris through steam big picture (in desktop mode) or game mode, which will let you access different steam controller configs.
Nope, Lutris was just running my games as desktop mode even if I was on gaming mode. I restarted and pressed the start/hburger button for a few seconds and saw a pop-up that said “Gamepad” and my control scheme shifted.
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