[ChristopherBuck]

Your question is pretty vague. Could you please provide more details as to what you are trying to accomplish, and what the problem currently is? Also, it would be helpful to know what language you are using to program the robot, so responses could be tailored to that language.

In theory, using encoders in autonomous would be just the same as using them in teleop. You first must open a reference to an encoder, indicating what DIO it is on and any other necessarry variables, and then use the supplied methods, functions, or nodes/SubVIs to start and count ticks to measure distance or rotations.