About EPUB files

Hi All

First please forgive me for my very vert bad English

I wont to sak about EPUB format in Calibre, i added the book to the library and made some changes in the book metadata and changed the cover and saved it
but the files always saved as three separated file one named cover.jpg
and the next is metadata.opf the the last is City of Bones.epub

i wont to copy the book to my not3 (it did not show as a device in the program)
but i need the EPUB (one file)
i tried to copy City of Bones.epub only it did not work (am using Aldiko on my not3)
i tried to copy the three files it did not work
i tried convert the file (EPUB to EPUB)and gave it new name but the concerted copy was a three files also

what should i do to get ONE EPUB file with the changes that i made

thank you in advance for your help