As long as you do a correct save to disc or send to device, the metadata should be correct.
If you manually copy the books from inside the Calibre library then you commit a grave sin and the immediate punishment is bad metadata. (Calibre updates the metadata in the books only when you save to disc, convert or send to device. The books in the library typically don't have correct metadata. The updated metadata is stored in metadata.db, not in the books in the library.)