There is not only one IDE
First, there are other good IDE options for Java development, the best known being Netbeans and Intellij. But don’t be afraid of the Eclipse.
Suitable version of Eclipse for Java EE
To develop in Java EE, my suggestion is to go to Eclipse downloads page and download the version Eclipse IDE for Java EE Developers. This is just a shortcut to get Eclipse Standard + JDT (Java Development tools).
The Eclipse works with multiple perspectives
Although you recommended "Eclipse Java EE", this does not mean that this version only allows you to create Java EE applications. Eclipse is an IDE that works with plugins.
A single installation can contain several of them and you can easily switch between different "environments" of development through the so-called "perspectives".
Accessing the "Javaee" perspective, the Eclipse will show the panels commonly used for Javaee development.
On the other hand, you could also install the plugin Pydev and switch to their perspective to develop in Python.
Anyway, it is not necessary to have more than one installation. Just do not overload Eclipse with many plugins as it may start to get slow.
Java SE and Java EE
In practice, there is no difference between developing for Java EE or Java SE. You will always create Java classes.
What changes are the Apis used, that is, interfaces you use to implement a program or auxiliary classes.
The biggest difference is that Java EE usually requires additional dependencies that do not come with the JDK, but are available through an Application Server such as Jboss or Glassfish.
Application Servers
Note that Tomcat is not a full JEE server, as it does not natively provide Apis like JTA, EJB, JPA, JSF, etc.
Because of this, he is known as a Web Container, that is, a Web Application Server that only provides web-specific Apis like Jsps and Servlets.
However, you can manually add third-party libraries to enable JEE Apis in Tomcat.
Additional help
If you have questions about the installation and basic use of Eclipse Kepler, take a look at my article:
Sid if any of the answers solved your question, please consider marking it as correct. Hug!
– utluiz