My main concern is getting rid of the extra files. There's a "saved" folder with a buch of subfolders in it, ie: audio, images ect and I dont want that but I cant seem to find that anywhere to get rid if it.

That's only what shows within your LW library. I don't know that there's any way to stop those from showing, apart from clicking the arrow to not expand Saved Files. Those subfolders (AFAIK) are just shown within your library for your ease of use... they're not separate subfolders created within your Saved folder.