Modding Skyrim on Linux
Getting Skyrim to play on Linux on its own is easy-peasy. Install it, enable the current Steam Proton version, and it will run. A lot of the value in Skyrim these days is the extensive stack of mods and the associated utilities that make them work. Getting those all to run isn't so easy, but it can be done, up to and including running the Creation Kit.
Steps:
1. Install Skyrim in steam.
2. (optional, but you really want this) Download the latest release of
Glorious Eggroll Proton custom. Create the directory compatibilitytools.d in ~/.local/share/steam and extract the Glorious Eggroll zip into it. End result should be something like ~/.local/share/steam/compatibilitytools.d/GE-Proton7-49. Close and re-start steam (it won't see GE until you do this).
3. Download
Mod Organizer 2 and extract it to ~/MO2 or somesuch. I have used Vortex before successfully but cannot currently recommend it, had lots of trouble getting it to not hang on Linux.
4. Use the "Add a game" option at the bottom-left of Steam window to add ~/MO2/ModOrganizer.exe as as game. Go to its settings menu and select 'force the use of a specific steam compatibility tool' and select the Ge-Proton7-49 (or whatever you're using).
5. Find the directory of the wine bottle created when you added Mod Organizer 2. This will be large randomly generated number under ~/.local/share/steam/steamapps/compatdata, something like 3525726694, three or four digits longer than all the other SteamIDs for games. Navigate to ~/.local/share/Steam/steamapps/compatdata/<yourMOsteamIDhere>/pfx/drive_c/Program Files/. There, create a link (ln, or right-click -> create new link to file/directory), with the name Steam, pointing to your Steam directory (usually ~/.local/share/Steam). Without this step, MO2 can't see your steam install, or the games installed by it.
6. At this point you should be able to start Mod Organizer 2. When the option to detect games comes up, it should detect Skyrim, and at that point Skyrim should be playable through Mod Organizer 2. Be sure to run it once normally (i.e. without SKSE) to set resolution, graphics settings, and create the initial .ini files Skyrim uses.
NOTES:
If you encounter audio problems (missing audio, awful echoing), go to the Steam settings for MO2, and set Launch Options: WINEDLLOVERRIDES="xaudio2_7=n,b" PULSE_LATENCY_MSEC=90 %command%
When you invariably need
SKSE, pick the version from their website that matches your version of the game, READ THE README, and extract the needed files to your Skyrim directory, generally ~/.local/share/Steam/steamapps/common/Skyrim Special Edition/. Restart Mod Organizer 2 and it should automatically detect SKSE, which will the be available from the big 'pick a program to run' dropdown in the top-right of MO2, which is usually titled "Skyrim Special Edition" by default.
If you need to install a vc++ redistributable, as more than a few utility mods require, copy the install file into your ~/MO2 folder. Run MO2, choose 'Open Instance Folder' from the folder button near the top center of the screen, and install the redistributable from there. This ensures it is installed to the same wine bottle that MO2 will run Skyrim from.
If you do some serious modding and need utilities such as BodySlide, Nemesis, SSEedit, MatorSmash, or whatever, install them like above. To run them, click on the 'choose a program to run' dropdown in the top-right quarter of MO2's screen and choose <edit> then click the + button to add an executable. Try them with default options, but you may need to manually set the 'start in' directory to "c:\Program Files\Steam\steamapps\common\Skyrim Special Edition\", which they should be able to parse thanks to the link made in step 5. Note the backslashes rather than foward-slashes, these paths are meant to be consumed by Windows programs running under an emulated Windows directory structure.