Print-on-demand services require that interior and cover files are submitted separately, but ebook services typically do not. Book covers will be included in your ebook (EPUB and MOBI) exports, but not in your PDF files.
Back matter is the stuff at the end of your book, after the main sections of the book are finished. Some common items in Back matter include: Epilogue, Index, Bibliography.
Back matter items are essentially chapters within a part, with one additional option to customize.