Back matter is material that is found, well, at the back of a book. Back matter includes sections that are not part of a linear progression of information and are therefore not expected to be read by all users of the book. It might also include one or more appendix sections, a glossary of terms, and an index.
An appendix is a collection of supplemental information at the end of a book. It is typically made up of reference material that does not belong in the main body of the book. This could be more detailed, in-depth information that is not necessary for using the product but is interesting to some users, or specialized information for optional features that not all users have.
To indicate their difference, appendixes ...