Insulate
both rails where new section connects to original layout completely isolating the yard electrically. Connect inside/outside, north/south, red/black wires from the main layout to AR1 and the output of the AR1 to the yard tracks.
The connection to the yard becomes polarity insensitive as it is reversing after all so don't use the same wiring scheme. Just try another nomenclature to describe the yard wiring (yard inside/outside, reversing north/south or blue/white) reducing confusion. AR1 will reverse polarity within the yard, any decoder equipped locomotives or cars there will simply 'go with the flow'.
If you are planning DCC controlled turnouts it may be helpful to wire those to the main buss, no reason to introduce potential confusion when the reverser trips...