Like I just said, you cannot use the stock O2 sensor setup with the EMS, it does not have the circuitry to drive them. Neither the upstream, nor the downstream sensors.
You can set up the EMS to use the #2 O2 input, yes. But the EMS only works with one O2 sensor at a time, as far as I can tell. It expects to see that input on the stock #1 wire. You can remap that in the .cal file so that it looks at the #2 input, or any of the other input pins on the EMS, but it expects to use sensor #1 for all it's functions, and I don't know of any way to change that or make a failover.
Chris
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