I am not sure I am correctly interpreting what you have written, so let me try to clarify.
Your shore power cable has three wires which are typically referred to as hot, neutral, and ground. Hot will carry 110v AC relative to the neutral (which is also called the return by some). Ground is used to establish a reference to marina ground. The neutral and ground are connected together at the marina source to establish the neutral, and should not be connected together anywhere else while you are on shore power. The isolator is installed in the ground wire path, not in the hot or neutral path. To install the isolator you connect a wire from the ground post of the shore power input connector to the isolator, then connect the output of the isolator to the original ground wire from the shore power connector. No breakers in the path except if the isolator itself has over current protection.
Hope that makes sense.