The Output frequency is the one that needs to be programmed, Here is what you want to know..
Output: Repeater Output That's heard on a radio
Input : The Frequency that's programmed into the repeater's recieve side or the radio to the repeater, Sometimes in some instances also referred to as the Simplex/Talk Around frequency where it bypasses the repeater so that dispatch doesn't hear..
Check out the wiki link above for more, Hope this helps..