There's no guarantee that anything official will ever be safe, and mods aren't officially supported. It's your risk to take, I'd make backups of characters & world files. And any other backups, if you're worried it might tank your system.

On windows it's as simple as:

1. copy bepinex files over to the valheim folder
   
2. chuck plugins into <valheim>\bepinex\plugins
   
3. run the game once (no need to load a world) and the mods will generate their default configs in <valheim>\bepinex\config

So you might be able to figure it out from that, I can't imagine it'll be all that different on linux. I know the bepinex release on thunderstore (use that, it's specific to valheim) has some .sh files, likely those will be involved. Hopefully someone who mods on linux will see this thread, good luck.