Since our team just started in Java, I was curious if we have to reconfigure the CRIO for it run in Java. If so, how do we do that? I know this probably a simple question, I just don’t know the answer. Any other beginners help is welcome too! 
Yes, you need to use the cRIO Imaging Tool to setup the cRIO for Java.
It takes only a few moments.
Just start the tool, click on Java Technology and Apply.
There’s no need to reformat.
Imaging cRIO
http://wpilib.screenstepslive.com/s/3120/m/8559/l/89727-imaging-your-crio
Getting started with Java
http://wpilib.screenstepslive.com/s/3120/m/7885