Mode S includes Modes A and C
Jodelman - I think you are confused. All Mode S transponders are required to reply to legacy Mode A/C interrogations, so obviously any "Mode S" transponder is really Mode A/C/S. Hence, to put Mode S into an aircraft that has a Mode A/C transponder, you remove the Mode A/C transponder and replace it with a Mode A/C/S unit.
Also, the squawk code is alive and well with Mode S. It still forms a primary part of the identification of the aircraft, along with the callsign (Flight ID), and is required anyway for interworking with Mode A/C interrogators.