1. There are seperate names for the controlls on the second remote. I can't remember them now, but if you look at the IFI aliases file you should be able to find them.
2. If you're using the VEX encoder it very simple. You need to connect your encoder output to one of the interupt ports on your robot. Then setup an intterupt handler that just increments a variable.
If you're using non-VEX quadrature encoders you should look at Kevin's encoder code from 2005(
www.kevin.org/frc/2005).