I would definately keep the current sensing to the battery line. I don't understand what a 50mv shunt is? I have heard of 50mohm shunts in series with the power line and paralleled to op-amps as a current sensor (that's what is on the boards that i'm testing this morning, actually). So as, say, 10A passes by, it generates 0.5v, the op-amp has a gain of ten, so 5v goes to the cpu's ADC... that sort of thing.
Total system design should take into account a maximum power and the input ratings should be specified accordingly.
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