You can setup a relay with yr ACC line which is switched on while the keys are turned, except when the engine is cranking (in most cars).
So, this will ensure that your second battery will be charged only when your keys are in the ignition but not when cranking which could cause high currents coming from yr tank battery. You will need a resistor inline with this cable to limit the charging current to the backup battery, the size of the resistor depends on the size of yr backup battery. As far as i understand your problem, that will solve everything.
HTH



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OK, I understand part of what you're saying, but not all. I will check out that ACC line, and maybe use dual 



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