No. On positon #1 all alt output goes to batt#1 ( assuming your HU/amps are hooked up to batt bank #2)Is your HU still hooked to batt#1? Most people forget about this. Are all 4 of your batt's the same kind ( flodded, AGM, gel)? Your setup is not ideal, but here's what I woudl do. Make sure all batt's are fully charged to begin with, start on both, then when you get to the cove, switch to #1 ( isolating yrou two banks, and will allow you to start on #1) Make sure there is no draw of your starting battery while runnign yrou stereo. I still like the idea of hookign everything ( stereo, boat electronics, ect) up to one bank of batteries and having a second battery hooked up ( thru perko switch) as emergency only.
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