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The isolator should have three studs on in - batt 1, batt 2, and alternator. Depending on the design, it may also have some control wiring.
The downside is that a true isolator is diode-based... so you take a ~0.7V hit constantly, and bad things happen when you fry a diode. I'm running Kussmaul Auto Isolators in two F150s (09 and 10) which use a control module and continuous-duty solenoid, to provide isolation for the on-board equipment. They work great and are less than $200 delivered. No voltage drop, either.