This phrasal verb has more than one meaning
Definition: to settle or solve a problem, disagreement or misunderstanding by explaining and discussing it.
E.g.1: I think this misunderstanding will be cleared up soon.
E.g.2: I know this is a difficult negotiation. Let’s clear the other points up, too. When we all agree we can go home.
This phrasal verb can be separated (E.g.2)