How to manually install Skyrim mods while using PlayOnLinux

The creation kit has now been released and can be found on Steam.

When we created Skyrim, we set out to make the largest, most engrossing role-playing game we had ever attempted. Now it’s about to get a whole lot bigger, thanks to our amazing modding community.

Mod-makers have a long history with Bethesda Game Studios, bringing to life new quests, locations and characters, as well as making changes to game from subtle tweaks to full-blown overhauls. With the Creation Kit, the same tool we used to create Skyrim, there’s almost no limit to what can be accomplished – and we’re putting that power in your hands. Best of all, access to the Skyrim Workshop and Creation Kit is free for anybody with a Steam account and a copy of Skyrim.

With the Skyrim Workshop, finding and installing your favorite mods is easier than ever before. Mod-makers will also enjoy a streamlined process for uploading mods directly to Steam.

Here is a link to the steam workship for Skyrim.

Source: Creation Kit Wiki

The best way to solve your problem is to unsubscribe from the Mods. In this way, Skyrim Launcher will no longer download them automatically.

To unsubscribe them, you needs to go to 'Data Files' on your launcher, then click on Skyrim Workshop and login to the Workshop.

From there, you should see your display pic at the right hand bar. Click on that, then click on Subscribed Items. You will see all the mods that your're subscribed to. Unsubscribe from those that you don't want any more.

You were unable to get rid of them previously from the 'Data Files' tab because all the mods are linked to your account. You have to manually remove them from the Skyrim Workshop.

I hope this helps! :)