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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.
(EDIT: realized you.already described much if this, blargh, im about to pass out and fall asleep)
Unfortunately I have been using Bazzite so long I'm not sure exactly how to explain how to do it on SteamOS, but...
So your Deck, when Steam is still running, is also running the layer that translates your joy and buttons and track pads and what not, as managed via Steam's controller profile system.
You can go into steam settings and find a button for something like a default desktop config.
You can uh, tinker with that profile and make it so a hot key or combo switches it over to just acting as basically an xbox369 controller.
When you are in that mode, Lutris, emulators run in desktop mode, etc... they should recognize your joy/trigger/button inputs as if they were a 360 controller now.
It... can be a bit confusing, but its not impossible to set up, at least not with the emulators Inhabe futzed about with.
Okay I reread what you said, tried it again and got it working. Thanks!
I’m in gaming mode, which is the weird thing.
Do you have steam running in the background in desktop mode or did you shut that down?
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.
So everything is working properly now.