you need a battery Isolator ...best way would be to have a setup where either motor will charge all the batteries ...there are Isolators than have input from 2 Altenators and then output to 3 Banks ....It sounds like your stereo and house bank batteries are parallel ... so to the Isolator will only see 3 batteries ... you might need 2 Isolators ...
Port motor would charge
1) port motor battery 2) Star motor battery 3) house Bank
Starboard motor would charge
1) Starboard Motor Battery 2) Port Motor Battery 3) Stereo Bank