Your DCS50 has two sets of DCC outputs. This means that you will be able to program decoders using one set of DCC outputs while the layout is running on the other set of DCC outputs.
When you hooked up your DCS50 to the layout, you used the RAIL A & RAIL B connections to the track. Now we will use the PROG A & PROG B outputs to set up a service mode programming track.
NOTE: The programming track is powered for programming only and cannot run locomotives. You will have to manually move your locomotive on to the track whether using the siding or isolated track programming setup.
Rear Panel Programming Track Hook Up Diagram
Your programming track can be as simple as a spare piece of track not connected to the layout as shown above or it can be a double gapped section of track connected to the DCS50's PROG A & PROG B outputs as shown below.
Programming Track Example Diagram