Well depends on the radio system, simply stated when people are talking on simplex, that is talking on the same channel as in CB radio. A two frequency simplex system is like this the Nebraska State Patrol dispatchers transmit on 42.460 mHz for general use, and the mobiles transmit on 42.300 mHz, for routine traffic.
Now a duplex system is set up like this, there is a repeater involved in most cases, it depends on the system but here is an example, the ham radio repeater I use the most transmits on 147.135 mHz and that is the frequency that the receiver (mobile) is set to receive on, or repeater output , when I push the button on my mobile to transmit the frequency changes to 147.735 mHz, which is 600 kHz above the receive frequency, this is the repeater input frequency. The repeater can transmit and receive at the same time (more about that later if you are interested).
With all that theory out of the way, and, to answer you question you want to program in the repeater output frequency, this is the way it works on conventional (not trunked) systems, I have no experience with trunked systems, the might work the same way I do not know, I don't have a need to know ...yet, however I would like to know for future reference however.
Does this help you at all? If not pm me