FWIW, it is more or less standard to have the shunt in the negative side in the battery monitoring systems that are installed in boats. (The Xantrex link series etc.)

This makes things a lot easier when there is more than one battery bank (engine cranking battery, generator cranking battery, house battery, electronics battery), particularly if the monitor is being retrofitted to an existing system which is often the case. There normally is (or should be) a common ground point for all the batteries and consumers and this is an easy place to install the needed shunts. Installations vary. Some monitor all batteries, others only monitor the house battery.