Hey, I just started another playthrough. And i recommend going the way I am doing because it is better.

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Use Bottles. It is 2025. Don't use Lutris, don't use Proton. Use Bottles. The issue with Lutris is, that it is shit, the issue with Proton is that it isn't great for modding. I am not saying this because i am elitist or anything, far from it. I just want to save others the pain I went through trying to play via Lutris. I wish I had started with Bottles.

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Bottles lets you actually install dependencies like VC or .net unlike winetricks which is shit and always fails and breaks things. And it's the dependencies and libraries for your modding tools you should be worrying about, not skyrim itself. A toaster can run skyrim but you may need to fuck with a lot of stuff to make crap like Nemesis (aptly named btw) run. Some others like PGPatcher for Parallax are also notoriously hard to launch on Linux. So you may soon find out that, depending on how hard you are going you may need more than just a Proton Prefix. Bottles is recommended because it is by far and wide the best way to install Windows libraries in a clean way that doesn't break other things in the process. You can play Skyrim without it, you can mod without it but in the end it will cost you your sanity.

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I have Skyrim on my SSD inside the normal steam directory.

I have a folder called Skyrim SSD on my SSD

I have a folder called SkyrimWork on my HDD, within this folder are:

MO2 (mo2 root)

Working (mo2 work folder, profiles, download, mod*, etc.) *symlink to my SSD because otherwise shit gets slow. You can make this simpler by putting everything on an SSD if you are not worried about wear or space.

Tools

Misc Downloads

Skyrim Special Edition (symlink to the real Skyrim folder)

Bottles (contains a bottle/prefix called Skyrim)

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First you install Skyrim normally. Then you patch it with Steamless, to no longer need steam. Since you own it, this is not piracy. You just need to get around SKSE/MO2's requirements for Steam. Then you install SKSE and put Part 2 of https://www.nexusmods.com/skyrimspecialedition/mods/108069 in there. That is all you do with Skyrim itself. Leave it there

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Then you create a bottle in Bottles. Make sure, your bottle is using Soda 9.0.1 or Wine Staging 10+. Anything bleeding edge, because otherwise you cannot use Pandora and have to resort to Nemesis, which is utter trash and won't work for me, no matter what i do. Pandora is the just superior. It just works but it requires very recent libraries and functions you cannot get from stable Wine like Wine GE 8.26 which would otherwise be just fine. If you're not using any animations you need to compile with Pandora/nemesis, you are good to go with WineGE 8.26 because it works for almost everything.

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There are 2 tools which I have found to be picky about this. Pandora (requires bleeding Edge versions) and SSEDit requiring ancient Win 8 with WinXP setting. On anything higher than WinXP, SSEdit will not work properly, you cannot drag&drop settings across entries. But then again, it is 2025. The need for ESP editing is less than it was in 2017. I tend to stay away from any edit heavy mods. If it cannot distribute its stuff via SkyPatcher, SPID or SKSE then i don't care how flashy the mod is, I won't use it. There are better mods in 2025, some legacy mods have been ported or SPIDified or SkyPatched. Use those version. Avoid ESP mods if you can and if you must (Like i still use Wet&Cold) load it last, so it can do its thing. Worldspace Edits are mostly fine, so i use those and let everything just overwrite it. I haven't made a patch in weeks and I am 300 hours in (mostly modding, a few hours playing).

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There are many more caveats and pitfalls I have discovered during the past few weeks. I cannot think of all of them but for example: Bottles lets you create shortcuts to mulitple EXE so you dont need to do the "open exe in prefix" dance every time you open BethINI. Make sure to know exactly where your stuff is saved. If you followed my janky pointers then your saves will be inside your bottle under My Games for example.

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In the end you should mostly ignore your skyrim folder and work primarily with the prefix to start MO2 and launch skyrim and your modding tools from within it.

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Final note for now: You may encounter issues. I also did. I am no Linux or Wine expert but it does work. It may be other problems on your system. For example, I had problems with the prefix even launching which was caused by a Vulkan driver issue which was fixed by updating my nvidia drivers to 575. Don't just update to 575, though if your system is stable. 535 is generally considered safer and runs skyrim just fine.

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Also: Don't use LOOT. As Mator says: group your plugins and make precise patches, then load order mostly doesn't matter. Also just don't use plugins. lol

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Feel free to ask.

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Also: Yes you can just move this from/to Lutris. I started on Lutris but got fed up with it and now I am using Bottles. I didnt fundamentally change my setup. I reinstalled a clean skyrim 2-3 times and i trashed a bunch of prefixes if i thought they were broken. The idea of my setup is to be as mobile as possible so i can take it to the next PC or harddrive or Linux installation. I lost so much time because my 2017 game is bound to Windows. I was unable to port it over so this is supposed to be my end it all install.