How do I allow a place along the boundary wire where my pet can safely cross?

To create the layout that you need, a double loop layout format will be necessary.

First, run the wire around the perimeter. When you get to the end, make a U-turn with your wire and backtrack around the coverage area.

Be sure to keep the wire 3 - 5 feet apart where you want signal. When you want to cancel the signal, bring the wires together and twist them 10 times per foot.