How do you set up the Talon SRX in position mode using the CTR absolute encoder

[rcdturtle]

We are trying to use a Talon SRX unit to control the angle of our pickup - shooter system. We have a VEX gearbox driving a chain gear that will have a range of motion of about 180 degrees. The encoder is mounted after the last stage so it should report the angle of the drive gear directly. While in manual mode, we are trying to move the gear in 0.5 degree steps (about 10 native units). When we enable the robot, the gear rotates part of a revolution and stops even though we have set the encoder position to zero and issued a talon.set(0) command in RobotMap. Is there someway to know where the encoder thinks the zero postion is. We are dealing with very small numbers because the set() command units are in rotations for position control. Should we be moving the encoder back a stage so the range of motion becomes 2.5 revolutions? If we do that, will the system still know where zero is? Is there an overall set up procedure for using the Talon SRX position mode with the CTR magnetic absolute encoder?
Thanks in advance for your help
Team 3534