Diamond says that it is important to differentiate between proximate and ultimate causes because it is not enough to understand proximate causes. In Chapter 3, for example, Diamond gives all of the proximate causes that allowed the Spanish to defeat the Incas. But understanding this is not good enough. We need to know why the Spanish had their guns and steel weapons and their epidemic diseases. If we do not know this, we do not really know what caused the Spanish to dominate the Incas.
We need to differentiate between these two kinds of causes because we need to know which causes are most important and which are simply results of other things. We have to identify the ultimate causes so that we can explain them, which will allow us to truly understand what causes certain conditions in history.