Hal effect current sensor question

The yellow wires are the AC output from the generator.  I don't know how your airplane is wired but generally speaking, to achieve what you want the sensor should be installed on the wire from the regulator output to the battery positive terminal.

The regulator output goes to the capacitor which then goes to the main switch so I think if I place it on he other side of the main switch that will do it.

It's hard to say without seeing a wiring diagram.  As long as the wire you choose to measure cannot carry current from the battery to a bus, and only carries regulator output to the battery or to a bus, it should work fine.

I think you mean Hall effect 

Yes … on the other hand most people would jump at the chance of having an effect named after them …?