I'm assuming by "pdt all in one" you mean Eclipse with PHP development tools? (I'd rather not have to assume--I'd rather you'd choose to TellTheDetails.) If you want to do Java development, it would make more sense to download one of the Java-oriented packages, no? If may already have the functionality you require, however (not sure, and I doubt it'd have the JEE stuff included).
If you want a JDK you should download one, and if you want a particular version, you should explicitly download it.
As David pointed out you would be better off downloading one of the Java-related bundles of Eclipse. Mainly because those bundles come with a lot of functionality that the PDT does not offer. And yes you can have both PDT and, for example, Eclipse for Java EE Developers, installed on the same system at the same it - just place them in different directories. That is what I do.
First, Eclipse PDT is a Java application so the fact that you were using PDT means you already had Java installed (either a JRE or the JDK). You can look at the Preference page - one of the entries here should tell you where the JDK or JRE is located.
It also sounds like you also added a few other plugins to Eclipse, enough to do some Java compiling and running Ant. Whether what you have is all you need I don't know, I gave up a long time ago trying to figure out what plugins I needed for Eclipse when the named Eclipse bundles started to come out (was it Callisto that was the first one? Can't recall...).
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