sorry, I wish there was an easy answer to that one, but unfortunately thats a tough one.
If the PID control works then you should be able to:
1. Turn PID control on for the motor in question
2. Set the target position for the encoder
3. Start the motor by setting a speed value.
So try this out. But bewarned, I feel the PID control for the 12V motors is somewhere between useless and broken.
I tried for weeks to get this to work and was never happy with it. It sometimes goes completely screwy. Be careful and test it out thoroughly before you rely on it. Also try at various battery levels.
And try not to set power levels > 75%.
If this doesn't work then you have to write the PID controller yourself or use some other control technique. Because the built in PID controller parameters can't be tuned.
Another suggestion...before you try to use the PID controller. Run the sample program "NXT Motor Consistency vs Time" its under Sample Programs/Motor directory. This will help you know that everything is working okay before pulling your hair out with the flaky PID stuff.