Nは presents what/who exists, focusing on where something/somebody is. On the other hand, the "Place に Ｎが あります" pattern(Lesson 6-1-2) focuses on what/who is there.
バナナは つくえの 上に あります。
As for bananas, they are on the desk/table.
犬は 木の 下に います。
As for the dog, it is under the tree.