Use the adjective upper to describe something that's the highest or top in position or rank. Your upper arm is above your lower arm, and the upper bunk on your bunkbed is closest to the ceiling.
Upper is useful for talking about anything that's located above something else. You might ski on a mountain's upper slope, taking the ski lift up as high as it goes, or become an astronaut so you can travel through the Earth's upper (or most remote) atmosphere. As a noun, an upper is the part of a shoe that's above the sole. And if you have the upper hand, it means you've got an advantage over someone else.