Don't know the answer to your question but you should have a battery switch that controls battery 1, 2 or both. Make sure you know which battery cranks your motor and run it on the way out. My understanding is that your electronics should all be hooked up to the other battery. Both batteries should be charged before going out but at least if they are not fully charged and you run down the "electronics" battery, you can still crank and go home.
I personally have my motor and GPS on one battery. Everything else on bat 2.
Anyone else have it rigged differently?