NetBeans vs Eclipse is a holy war question. I say this not because I think it's a bad question that should not be asked but because most of the time holy wars mean that the two pieces of software are equal enough that you should just pick one and start using it. Personally I've picked Eclipse since it was what was used at my last job and it's what I see used most of the time. Use what works and try the other every so often to make sure what you're using did not fall behind.
Scala vs Groovy is simple if you know what you are aiming to do. Groovy is more designed to be scripting language and Scala is more designed to be a next generation OOP language. So if you are looking to quickly write scripts use Groovy if you are looking to write code that will stick around for a while and will be part of your actual application use Scala. Long story short, Scala will best help you in Java EE work.
In a way, this all misses the point. If you want to be an awesome Java EE programmer (as your name implies) I would start looking at frameworks in Java, not languages built on top of the JRE like Groovy and Scala. While some big names have started using Scala (like Twitter and FourSquare) most people don't have any reason to stray far from standard Java to get their work done. You will be far more marketable if you can use Spring or Hibernate then if you knew both Scala and Groovy.
Also be awesome in core Java before you learn other stuff. There are lots of cool shiny toys that run on the JRE so it's easy to get distracted. Just remember that if you are good at the core Java ideas (or core programing ideas for that matter) you will be able to pick up anything you need very quickly.
If you are just getting started I would recommend starting small and learning some Ant. It's the standard language for Java build scripts. Learning it will both give you a useful skill in common Java software and teach you the ins and outs of the Java compile process. Two warnings 1)It's a headache if you try to do anything impressive in it so stick to building simple apps. 2)Don't expect it to mean much on a resume, basic Ant knowledge is just a useful skill to have as a Java programmer.
If you now want to know what framework to learn that's a whole other holy war question. I recommend you look at jobs in your area and pick something everyone seems to be using that sounds fun.