Adjusting Saving preferences

How can I set where Scrivener automatically saves files and templates? It’s just dumping them in the root of my documents folder.

It doesn’t actually automatically do that. It will save projects precisely where you created them when using the wizard. As with many applications, once you use the save tool at a certain location, Scrivener will remember that location in the future. But if you have never used the line which determines where the project is saved, it will still be at the default location which is Documents. Feel free to move existing projects wherever you like. Scrivener doesn’t care where they are (just don’t move them while they are open).

Are you positive templates are being saved in Documents? That shouldn’t ever happen. When you use the save to template menu item, it doesn’t even ask you where to put it because those all need to go in a special place in the Library folder.