Save changed metadata to the file in the library

When I add a new book (epub or pdf) and edit the metadata I would to like to save the changed metadata directly to the library file.
How do I do this?

At the moment the metadata is only written into the calibre database but not stored into the ebook file.

That's a problem, because when I load the ebook through the calibre content server to my Transformer Prime (used App: Aldiko) the ebook on my device has no title, author or tags.

So how do I save the metadata in the ebook file after editing the metadata in calibre?