SEIV on Steam: where should I place mods?

[Suicide Junkie]

More specifically:
Se4\data is where the stock data lives
Se4\ModName\data is where the data for the "modname" mod lives

Se4\savegame for the stock saved games
Se4\ModName\savegame for the mod saved games.

And so on...
When parts are missing from the mod folder, then SE4 uses the stock files and folders as a fallback; most mods don't change everything, so this saves hassle.

The only thing that should ever replace stock files is an official patch, or the imageModPacks, since they are designed to be 100% backwards compatible and do not invalidate savegames or change any mechanics.