I've been mostly developing web apps with Drupal 7 and CakePHP the past few years. My recent experience has been with MYSQL, PHP, and then front-end languages on top of that.

Soon here I'm hoping to make the move into java development with my company (using Java EE 5-7).

I understand object oriented programming etc etc but Java EE is something I don't have much experience with. I'm certain I can learn it and pick it up quickly...

Any recommendations on how to learn this or what tools to learn that may be helpful for java ee?

You should look into jsf with like richfaces, primefaces or icefaces for the interface components.
As for the technologies you could look into managed bean, project dependencies with graddle, context dependency injection with like spring, a database persistence framework like hibernate. Make sure you always look into annotations configurations over xml/properties.

Once you got that working, you can support multi languages with resource bundled properties and start adding logging with with log4j.
You could look into AOP to handle your logs if you're looking for more advanced stuff.

Easiest way to learn is start with a minimal amount of page but to implement all the cool techno.

I've learned a lot about persistence and so on lately so I'm hoping to begin implementing cool frameworks like hibernate and so on to help make everything *easier.*

I guess I should figure out what exactly my company uses -.-