Basically, the only files you need (or should have) in your Mods folder and its hierarchy are .package and .ts4script files. The program knows where to look based on the Resource.cfg file which should be in the top level Mods folder. The script files (.ts4script) should not be in any folder deeper than one level of the main Mods folder, so you can have .ts4script in /Mods or /Mods/foldename but no deeper i.e. if you put them into /Mods/foldername/anotherfolder they wouldn't be picked up. As stated, also, related script and package files should be kept together.
Hope this helps :)
