This has been asked several times.
The input is the freq. the radio transmits to the repeater. The output is the freq. coming out of the repeater. Obviously they can't be the same or it would throw itself into a continuous loop and hear nothing but its own signal.
Generally you want to program in the output. Otherwise the scanner could stop on the input freq. which is much lower in power and signal level causing you to miss traffic.
mancow