The physical location of the shunt does not matter, but it should be the last thing connected between the negative battery post and any other wiring. If you want to continuously monitor the current going and coming from several different power sources and loads, you will need several shunts and several meters (or a way to switch between them). Usually though, these different paths are something you want to check once in a while, or when something appears to be not working correctly.
For that, a DC clamp ammeter is far more useful. This device clamps around any wire you can access, without having to disconnect or otherwise disturb the circuit. The better ones will read from 10 milliamps to 200 amps DC (also AC, if you are debugging AC circuits). They usually also include standard DVM type functions, so it is the only electrical test instrument you need. The Fluke 325 is a premium example, the Extech 380941 is another good one (I own both of these). There are cheaper ones that work OK, just make sure it reads DC amps and has resolution of at least 20 or 30 mA. For debugging DC power systems and also understanding what is using power, these meters will save you hours or days of work. Simply clamping the jaws around any wire will give you current magnitude and direction instantly. They generally have MAX/MIN functions as well.