The mods just go into the data folder and then you can (sometimes) enable them in-game througu the Creation option. I don't know if or where it would store the settings inis, but you can also edit the loadorder txt file to manually enable them by just adding 1 .esp or .esm per line in the order you need them to load in.

Even on Windows, enabling them in-game can be fucked up, tho. I always have to do everything manually to get things working 100%.