In the future, the easiest way will probably to be Nexus Mod’s new native app. But that’s still in alpha.
I’ve found it simplest to just manually copy the mods into my install folder and add all the .esp’s to my Plugins.txt.
To make the game start with SKSE on Steam, I would rename SkyrimSELauncher.exe to SkyrimSELauncher.exe.backup and rename skse64_loader.exe to SkyrimSELauncher.exe. But I rebought the game on GOG and use the Heroic Games, which let’s me change which exe to run so I don’t have to rename things.
Another thing to keep in mind when installing mods is that Linux uses case-sensitive filesystems. That means the folder skse is different from SKSE. Some mods use lowercase, other mods use uppercase. But Skyrim will only recognize one of these folders, so you would have to rename the folder before merging it into your skyrim install folder.
I’ll also say that I never did any major modding. I’ve used maybe at most 2 dozen quality of life mods.
My shameful recap includes the week I tried to switch to MacOS with the M4 Mac Mini. But I ended up hating MacOS.
Trying to use SteamTinkerLaunch to install Nexus Mods was a nightmare for me. It was so bad that I wiped my Linux install and installed Windows.
That Windows install didn’t last long, but ever since I’ve just done things manually. I’m going to keep doing that way until NexusMods.App is ready.