1.) The EXT IR Input on the S12 is solely there to enable IR routing on the 14 IR outputs. There is no control of the S12 through this port.
2.) You will need to wire directly into the keypad inputs using an RP6 or SR1 as mentioned above.
3.) The IR Macros for an S12 aren't that bad, it's only one step, the source command. All video switching will track the audio source.
4.) The best way to do multi-zone control is by using RS232.