A mechanical encoder typically has three pins: a phase A, a phase B, and a common. When wiring up an encoder to the RC, you would connect the phase A and phase B to two separate digital inputs, and then connect the common to +5. Optical encoders has a similar pinout, but with a connection for ground, too. Kevin Watson (
http://kevin.org/frc) has an example of how to read an encoder in programming, but I'm guessing from the terminology that you used that you've already seen this code. I couldn't really understand what you were asking, but I hope that answers your question.