Both Managers use a Virtual Folder System that prevent corruption of the game's data folder. Many of us Modding Veterans used to manually install our mods and when Mod Organizer 1 came along, it was like a weight was lifted from our shoulders. Using Vortex or Mod Organizer 2 removes that step by remembering what is over-written by what.
If you add one mod and then another mod wants to Over-Write files of another mod, you have to keep track of what files get over-written in case you want to reverse that and restore those files. It's best to use a Mod Manger program like Vortex or Mod Organizer 2 for your mod installations.
