You should NOT look inside the Calibre library. And you should definitely not copy any books from there.
Use the Save to disk feature. Then you decide in the template exactly how the book should be named.
But this only works if the different fields for the books contains correct information. The title should only contain the title, and not any series information. The series information goes in the series fields. If you have some extra information you wish to store, you create a custom field.
If you use Calibre as intended, you will hopefully be less frustrated. But it may take some time before you get the hang of it. I suggest you do some experimenting to understand Calibre better. Try to get metadata from the filenames. Try to set all fields perfectly. Try fetching metadata for the book. Try to save to disk using different templates. Try the plugboard to see what it does.