If you're nontechnical maybe I should introduce you to the term metadata. That's all the information calibre is so good at displaying and manipulating; the publisher, the series name and volume number, the cover thumbnail etc. Metadata is everything about the book that isn't the book itself.
Unlike when you load a book by copying it manually, cc retrieves the metadata for each book as calibre transfers the book, and cc builds its own database so it can show you the metadata, let you sort by series, etc. So if cc doesn't get the book from calibre, it doesn't get the metadata, doesn't make an entry in it's data base and doesn't know the book is on the device.
If the book you manually loaded is already in calibre, just select it and send it to device using calibre. You can delete the copy you transferred manually.
And I'm sure you've figured it out already, but you can use virtually any ebook reader that supports the ebook file types you have. You could even have one app open epub files and another open pdf files.