Projects are confused about associated files

I have two projects that have become intertwined because I created a template from one project and used it to create a new one.
I did this because when I started a new project from scratch, all the questions I had to answer made a book with different fonts and formatting that I did not want.
Now, however, I cannot get the new project on my bookshelf with a new cover, but the old book opens the new file. How do I get this straightened out?
And, in the future, how can I create a template that recapitulates my previous simple formatting that isn’t changed because the Papyrus makes me put in a bunch of info about my project that doesn’t make sense, because I write non-fiction that doesn’t fit into your set categories?
Thanks for any help you can give.