As far as I know, Web Tools Project is an add-on for a regular Eclipse, that adds all features to turn it in to Eclipse for Java EE. (please correct me if I'm wrong). So my questions are:
Is it better to have 2 Eclipses (1 regular, and 1 for Java EE), or is it better to simply install Web Tools Project in my regular Eclipse?
What is the difference between Web Tools Project, or Eclipse for Java EE?
With Web Tools Platform you are also able to develop Java SE applications, just clicking one button - change perspective(if you want) and it becomes like Eclipse for Java SE. So you dont need to have 2 versions of Eclipse. IAlso this conversation can be helpfull for you What is the difference between Eclipse for Java (EE) Developers and Eclipse Classic. In main case it's the same thing only including extra tools for developing EE applications. Any time you can extend it using plugins. So I recommend you download and install Eclipse IDE for Java EE developers which already includes the Web Tools Platform (WTP)