Not sure if you're still looking but inside your steam bottle in the steam folder there'll be a folder called SteamApps. Inside that is common inside that is your Skyrim install. As for nexus. All of my mods are from nexus and they work beautifully. :D
Side note - I had to reinstall due to the crossover 14 upgrade, and found that SKSE would no longer work after a successful install - however, I was adding the skse_launcher.exe to the crossover apps via the run command... interface.
What worked was using the run command... interface to run the shortcut that the SKSE installer creates in the crossover user's desktop folder
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