Mantano's Handling of Books
From what I can tell, Mantano does not make a copy of the book. Mantano does not automatically scan for books, like some other e-reader software. The user must import individual books into Mantano. During the import process, Mantano reads the metadata from the book and stores a pointer to the book's location in it's own database. You can see this pointer in the information you get when you long-press on a book in the book-list.
I tested this by deleting a book outside of Mantano. Mantano still showed the book in it's list because it was only displaying the information from it's database. When I tried to open the book, Mantano reported the book as missing and gave me the option to delete it from the book list.
For myself, when I finish reading a book in Mantano, I will remove it from the book list, but leave it on the device (Mantano gives you this option). Later, I will let Calibre delete it from the device. I think this is a clean way to do things.
I will, however, post a request in the Mantano thread, asking that they add a means of validating the book list, identifying those books that are missing and offering the user the option to delete them.