You don't (and should never) change the Library naming structure. (See the FAQ) Or even add books directly.
There is a process that ADD performs on every book (just like any public one does). The files name is logged into the Catalog (the DB) as part of this.
The file templates are for EXPORTING to OTHER devices, not internal use.
Those are usually quite capable of delivering books from the GUI in just about any combination.

See the Metadata plugboard for devices that do not use filenames for their bookshelf manager (that is many, these days)