Αυτό/αυτά is this/these respectively and you use it when you're talking about something close to you, or something you're pointing at. That/those is εκείνο/εκείνα and you use it when something isn't so close, or to distinguish something from another. So, you could say "Αυτά είναι τα βιβλία μου, εκείνα είναι τα δικά σου." -> "These are my books, those are yours.".
I thought that I'd been told that εκείνος can only be used transitively: εκείνος ο σκύλος είναι καφές, but not εκείνος είναι ο καφές σκύλος. Is this incorrect?
I'm not very good at grammar, so I'm not sure about 'transitive/intransitive' in this context. Anyway, εκείνος -η -ο/εκείνοι -ες -α can be used just like that/those. So both sentences are correct (except that the adjective καφέ—i.e. the color brown—is indeclinable, and so it would have to be εκείνος ο σκύλος είναι καφέ and εκείνος είναι ο καφέ σκύλος - that dog is brown and that is the brown dog).