Oh I also wanted to mention that once that mod manager has installed the mods you don't need it to ensure the mods are being used, I'll typically launch from the usual launcher and only load the mod manager when I'm actually seeking out mods since some how it interferes with a 3rd party injector that gives me proper menus in triple screen resolutions. So yah you can totally run the mod manager to soak up and activiate mods and then shut 'er down and load normally, the mods will still be in play.
Downloading manually is much easier. The Nexus Mod Manager is the most useless thing I've ever seen since the invention of the back scratcher.
You know how I know you don't use a lot of mods that at this point are starting to really overlap with one another? I used to install mods manually like you, but then I something something knee.