the biggest difference to Windows gaming is that for Windows games on Linux played via Proton every game gets its own Proton/Wine prefix (basically a windows folder structure)
ifyou want to use mod manager you need to run them inside the game specific proton prefix

Steam Tinker Launcher simplify this process

Yeah modding is basically the same assuming you don't have to use some kind of installer for them then it would be a bit more complicated, however I'd imagine using wine would solve that for the most part (haven't installed mods through an installer on Linux so can't speak much on that)

And also you might need to learn where Linux stores those game files but you can always just use steam to directly open the game folder