nuge, is your question based from hunting from a stand? Height wil have something to do with it as well as distance to the deer. If the deer is broadside to you and you are at a steep angle to him, then yes, you may have to aim at the top half of the deer in order to take out both lungs. If the deer is further from you or ground level, then you may be OK with shooting the bottom 1/3 of the body. Each situation is different. I find the "shoot for exit" to be most valuable when shooting at a quartering away angle. And yes, you have to plan to shoot where you want the arrow to come out the opposite side of the deer.

Here is an excellent reference book which helps show where to shoot. As you can see from the cover, it shows north american animals in natural positions, with their internals drawn in. It also refences aiming points in many different positions.

http://www.safaripress.com/1-57157-267-8.html