It shouldn't matter where skyrim is installed, you should put mods inside the "data" foulder located inside your "skyrim" one. The file path depends on the texture/mesh/sound/etc you are replacing. Usually when you download somebody else's mod they will already have created all the necessary subfoulders and you'll find inside their archive either a data foulder (which you should simply merge with yours) or a texture/mesh/whatever foulder which you should put inside your data one (sorry, I'm phrasing it quite badly). When making your own mods you should check the bsa files for the correct file location. Hope this makes sense. I'm sorry. I feel like this is exactly what I did. It's no different than Oblivion or Morrowind mods, right?