Eclipse consists of a base
IDE and a long list of plug-ins. On the Eclipse website, there are several packages available. Some of the packages contain more plug-ins than others.
The Java EE version contains the base IDE plus a number of plug-ins for Java EE development. You do not need to unzip both those ZIP files; if you want to do Java EE development, just use the Java EE version.
Even if you installed a different version, you can install additional plug-ins in Eclipse later, by going to the Help / Install New Software menu.