If I import stuff into UE4 from a completely separate folder. Will UE4 still save a copy of it in my project folder (like inside the UE4 assets file?)? I just have a little ocd when organizing things like this.
Yes, when you import something it will be brought into the engine and saved as a unreal asset file. You can keep your source files organized elsewhere, it will also reference that location of the source file when you want to make a change and reupload the file.