I'm not sure the NMM works for Witcher 3. Anyway, the game is quite mod friendly. Installing manually is just a matter of creating a "mods" folder inside the game's root folder (GalaxyClient\Games\The Witcher 3, or Steamapps\Common\The Witcher 3), and then pasting the mod there. Organization isn't hard since all the mods are contained there, and you usually only have to copy paste a folder (like "modScabbards" for a scabbard mod, or "modTurbolighting" for the enhanced Lighting mod, "modAutoApplyOils", etc) and it just works.