Calling all battery experts….

A few years ago I replaced my battery charger with a 3 bank pro charger. It has one set of leads for the start battery and one set each for the two house batteries. The leads on the charger have a label that states they should be attached directly to the battery. The problem is I’m putting in a battery monitor, and that requires all neg leads to go thru the shunt… I don’t understand why the neg. leads have to go to the individual battery. As installed now the house batteries are…Calling all battery experts….