For those who don’t know, Proton is the tool that the deck uses to run windows games on Linux. GE-proton is an alternative build of proton that includes extra fixes for games, media codecs to fix video playback, and more. You can easily install GE-Proton by going to the discover store in desktop mode, installing ProtonUp-qt, and then selecting GE-proton from there.
The way that GE-proton is improving mod support here is by recognizing common mod launcher .exe files such as skse_loader.exe. If it sees a mod launcher executable in the game folder it will use that instead of the original game launcher.
If you have GE-proton installed, you can easily select it for any steam game by opening the game properties, checking “force compatibility tool”, and selecting the GE-proton version you want.
The tool ProtonUp-qt will also let change the setting per game as long as steam is closed. Just open “game list” and set the proton version per game.