The ROBOTC team is in the final stages of testing version 3.06, which includes support for the new encoders (among other things). We know that many of you have the physical encoders and are just waiting on software support, so we have an early version you can download here: http://www.robotc.net/files/ROBOTCforCortexPIC_306.exe
If all goes as expected, this will be final version.
Documentation on the new features and how to use the encoders can be found here: http://www.robotc.net/blog/2012/02/08/programming-with-the-new-vex-integrated-motor-encoders/
Built-in PID and Target Distances are not yet supported, but are planned for the near future.
Feedback is welcome and appreciated, especially during our testing phase.