My guess is that you need to invert the outputs going to one set of motors (left or right).
For example, if you were to tell all motors to drive fwd by sending them the same signal, and they were all wired identically, they may ball rotate their output shaft in the clockwise direction. They are all traveling in the same direction, but they are mounted on the chassis in different orientations (the right motors are rotated 180 degrees from the left), so this results on one set driving fwd and the other driving backwards.
To test what needs to change in your code, take baby steps. Verify the motors on the right had side travel fwd when you press fwd on the joystick. Then do the same for the left motors. If one side is going in the wrong direction, invert the output being sent to the motor controllerscontrollers for that side of the drivetrain (multiply output value by -1).
If that doesn't resolve the problem, providing a copy of your drivetrain code, and a description of how the turning isn't working specifically will help us narrow it down for you guys.
If you haven't seen it already, there's a good collection of information on java programming here:
http://wpilib.screenstepslive.com/s/4485/m/13809