I actually don't sort mine out. When I do a book, I like a consistent look, so I want to use only templates from the same set (plus it narrows down my choices so I don't have as many decisions to make). I keep mine together just by the "set" it's a part of.... like for example... all of Amy's Project Grids are grouped together in one master folder. I do keep each subset in its own folder as well, since after working with them for a while, I know basically what is in each set and I find it easier to go to that subfolder and find what I need vs. scrolling through one large folder with lots of stuff in it.
If I liked mixing and matching templates more, I would probably organize differently but since I like to work within sets, this works well for me.