First, I'd highly recommend not maintaining seperate ground planes. This is a safety issue more than anything. With two seperate ground planes, you could call one ground (ie engine block) and the other would be considered "floating". The issue is that static charge can build up between these two ground planes and since they aren't shorted together ... then there is nothing to ensure they don't build up a voltage between them. So now, two wires which you think are at 0V are actually at different voltages from one another ... and you could be shocked. Maintain only one DC ground plane, it's the right thing to do.
As for measuring only house battery current ... just connect the shunt to the (-) terminal of the house battery. Connect _nothing_ between the (-) battery terminal and the shunt. The terminal on your shunt that is connected to nothing at this point (the _other_ terminal) can now be considered the (-) battery terminal for this "battery" (which is now a combination of battery and shunt). In this way, you ensure that the current passing through the shunt is exactly the same current passing into the house battery.
1981 C&C 32