I am a beginner. I am using Aptana Studio for PHP. Today, I also downloaded Eclipse. I notice most of the features and workings are similar. It seems that one is built on the code-base of the other.
If so, what was the need for two similar Open Source IDEs on Java?
Aptana is built on Eclipse.
Eclipse is a general-purpose/Java-focused editor, whilst Aptana offers additional features which are targeted specifically at web development.
There are also other Eclipse plugins that also focus on web development, including the Web Tools Project from the Eclipse team.
Some people like Aptana, finding it a convenient mix of relevant tools. Others find Aptana too intrusive, and prefer to individually select their own plugins for JavaScript, CSS, XML, and so on.
what was the need for two similar Open Source IDEs on Java.
Variety is the spice of life. There are plenty of others IDEs other than just these two, and the same situation applies to most software, and tools/technologies in general.
Generally, different tools don't have the same focuses, and therefore varying benefits for different users.
This is especially true in the Open Source world, where users can easily customise and re-release products to work in the way they want.
You might wonder why the developers of Aptana built a "new" IDE based on Eclipse rather than simply working on Eclipse plugins.
The reason for this is that there used to be a paid-for Pro version of Aptana. This no longer exists however; you can get all the Aptana features now in the free Community Edition.
If you are searching for an free / open source IDE for PHP development i suggest Eclipse. If you can give some money to some company i suggest you give a try PHP Designer. PHP Designer supports as you guess PHP and debugging, also javascript framework like jQuery.