Sounds like PO revamped your wiring.
I can assure you that Beneteau wired the boat from the factory to include a starter bank and house bank with the appropriate switches to isolate the two banks. I have chartered several Beneteaus, including two different 331's, and they were all wired as described above. I would advise reconfiguring the wiring back to the original design. Regardless of how big of a house bank you've got, if the house bank discharges or there is a house bank problem, with the boat configured to the original factory at least you will have a dedicated starter battery isolated from the house bank to get you home. If you have some skill with basic wiring, this is a job that you can do, especially since the switches are already installed. If you don't feel comfortable, hire a marine electrician to bring the wiring back to factory specs. Something that you may want to consider is installing a switch to combine the starter and house banks in the event the starter bank discharges inadvertently (forget to turn off the starter bank when cruising/anchoring).
From your description of your present bank, you probably have two 4D batteries (approximately 400 amps). Even with a sizeable house bank, I wouldn't take a chance and not have a dedicated starter battery.
