If you do it manually, yeah it’s something like

~/.local/steam/steamapps/common/StardewValley/mods

SMAPI has a .sh in their release zip that sets it up for you, and their wiki is pretty solid if you’re wanting to do it through proton instead of the native application. I gave the nexus mod app a try, works pretty well but without premium you need to download mods individually, having an actual mod manager is nice though.